Job request: 14272

Organisation:: University of Bristol
Workspace:: post-covid-mentalhealth
ID:: m4gv65bahdh7pdb7
This page shows the technical details of what happened when authorised researcher Venexia Walker requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.
Jobs

Action:

make_model_output

Status:

Status: Succeeded

Job identifier:

ebcf6tardgjbol6e
Pipeline

Show project.yaml
version: '3.0'

expectations:

  population_size: 200000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project_actions.R 
  ## Edit and run create_project_actions.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Generate vaccination eligibility information 

  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 prelim study_definition 

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

  ## Generate dates for all study cohorts 

  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

  ## Implement study_definition for prevax 

  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

  ## Implement study_definition for vax 

  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

  ## Implement study_definition for unvax 

  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 

  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 

  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 

  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

  ## Stage 1 - Data cleaning - all cohorts 

  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

  describe_file-input_prevax_stage1:
    run: r:latest analysis/describe_file.R input_prevax_stage1 rds
    needs:
    - stage1_data_cleaning_all
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_prevax_stage1.txt

  describe_file-input_vax_stage1:
    run: r:latest analysis/describe_file.R input_vax_stage1 rds
    needs:
    - stage1_data_cleaning_all
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_vax_stage1.txt

  describe_file-input_unvax_stage1:
    run: r:latest analysis/describe_file.R input_unvax_stage1 rds
    needs:
    - stage1_data_cleaning_all
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_unvax_stage1.txt

  ## Stage 5 - Run models 

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

  cox_ipw-cohort_prevax-main-addiction:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-main-addiction.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-addiction.csv
    needs:
    - make_model_input-cohort_prevax-main-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-addiction.csv

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

  cox_ipw-cohort_prevax-main-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-main-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-main-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-anxiety_general.csv

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

  cox_ipw-cohort_prevax-main-anxiety_ocd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-main-anxiety_ocd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-anxiety_ocd.csv
    needs:
    - make_model_input-cohort_prevax-main-anxiety_ocd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-anxiety_ocd.csv

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

  cox_ipw-cohort_prevax-main-anxiety_ptsd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-main-anxiety_ptsd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_prevax-main-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-anxiety_ptsd.csv

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

  cox_ipw-cohort_prevax-main-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-main-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-depression.csv
    needs:
    - make_model_input-cohort_prevax-main-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-depression.csv

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

  cox_ipw-cohort_prevax-main-eating_disorders:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-main-eating_disorders.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-eating_disorders.csv
    needs:
    - make_model_input-cohort_prevax-main-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-eating_disorders.csv

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

  cox_ipw-cohort_prevax-main-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-main-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-main-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-self_harm.csv

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

  cox_ipw-cohort_prevax-main-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-main-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-main-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-main-suicide:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-main-suicide.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-suicide.csv
    needs:
    - make_model_input-cohort_prevax-main-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-suicide.csv

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

  cox_ipw-cohort_unvax-main-addiction:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-main-addiction.rds --ipw=FALSE
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-addiction.csv
    needs:
    - make_model_input-cohort_unvax-main-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-addiction.csv

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

  cox_ipw-cohort_unvax-main-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-main-anxiety_general.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-main-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-anxiety_general.csv

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

  cox_ipw-cohort_unvax-main-anxiety_ocd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-main-anxiety_ocd.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-anxiety_ocd.csv
    needs:
    - make_model_input-cohort_unvax-main-anxiety_ocd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-anxiety_ocd.csv

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

  cox_ipw-cohort_unvax-main-anxiety_ptsd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-main-anxiety_ptsd.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_unvax-main-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-anxiety_ptsd.csv

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

  cox_ipw-cohort_unvax-main-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-main-depression.rds --ipw=FALSE
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-depression.csv
    needs:
    - make_model_input-cohort_unvax-main-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-depression.csv

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

  cox_ipw-cohort_unvax-main-eating_disorders:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-main-eating_disorders.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-eating_disorders.csv
    needs:
    - make_model_input-cohort_unvax-main-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-eating_disorders.csv

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

  cox_ipw-cohort_unvax-main-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-main-self_harm.rds --ipw=FALSE
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-main-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-self_harm.csv

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

  cox_ipw-cohort_unvax-main-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-main-serious_mental_illness.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-main-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-main-suicide:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-main-suicide.rds --ipw=FALSE
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-suicide.csv
    needs:
    - make_model_input-cohort_unvax-main-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-suicide.csv

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

  cox_ipw-cohort_vax-main-addiction:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-main-addiction.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-addiction.csv
    needs:
    - make_model_input-cohort_vax-main-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-addiction.csv

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

  cox_ipw-cohort_vax-main-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-main-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-main-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-anxiety_general.csv

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

  cox_ipw-cohort_vax-main-anxiety_ocd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-main-anxiety_ocd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-anxiety_ocd.csv
    needs:
    - make_model_input-cohort_vax-main-anxiety_ocd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-anxiety_ocd.csv

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

  cox_ipw-cohort_vax-main-anxiety_ptsd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-main-anxiety_ptsd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_vax-main-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-anxiety_ptsd.csv

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

  cox_ipw-cohort_vax-main-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-main-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-depression.csv
    needs:
    - make_model_input-cohort_vax-main-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-depression.csv

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

  cox_ipw-cohort_vax-main-eating_disorders:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-main-eating_disorders.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-eating_disorders.csv
    needs:
    - make_model_input-cohort_vax-main-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-eating_disorders.csv

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

  cox_ipw-cohort_vax-main-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-main-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_vax-main-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-self_harm.csv

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

  cox_ipw-cohort_vax-main-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-main-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-main-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-main-suicide:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-main-suicide.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-suicide.csv
    needs:
    - make_model_input-cohort_vax-main-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-suicide.csv

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

  cox_ipw-cohort_prevax-sub_age_18_39-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_18_39-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_age_18_39-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_18_39-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-depression.csv

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

  cox_ipw-cohort_prevax-sub_age_18_39-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_18_39-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_age_18_39-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_18_39-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_age_18_39-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_18_39-anxiety_general.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_age_18_39-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_18_39-depression.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-depression.csv

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

  cox_ipw-cohort_unvax-sub_age_18_39-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_18_39-self_harm.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_age_18_39-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_18_39-serious_mental_illness.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_age_18_39-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_18_39-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_age_18_39-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_18_39-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-depression.csv

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

  cox_ipw-cohort_vax-sub_age_18_39-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_18_39-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-self_harm.csv

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

  cox_ipw-cohort_vax-sub_age_18_39-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_18_39-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_age_40_59-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_40_59-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_age_40_59-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_40_59-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-depression.csv

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

  cox_ipw-cohort_prevax-sub_age_40_59-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_40_59-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_age_40_59-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_40_59-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_age_40_59-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_40_59-anxiety_general.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_age_40_59-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_40_59-depression.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-depression.csv

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

  cox_ipw-cohort_unvax-sub_age_40_59-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_40_59-self_harm.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_age_40_59-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_40_59-serious_mental_illness.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_age_40_59-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_40_59-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_age_40_59-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_40_59-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-depression.csv

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

  cox_ipw-cohort_vax-sub_age_40_59-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_40_59-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-self_harm.csv

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

  cox_ipw-cohort_vax-sub_age_40_59-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_40_59-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_age_60_79-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_60_79-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_age_60_79-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_60_79-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-depression.csv

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

  cox_ipw-cohort_prevax-sub_age_60_79-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_60_79-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_age_60_79-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_60_79-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_age_60_79-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_60_79-anxiety_general.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_age_60_79-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_60_79-depression.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-depression.csv

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

  cox_ipw-cohort_unvax-sub_age_60_79-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_60_79-self_harm.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_age_60_79-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_60_79-serious_mental_illness.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_age_60_79-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_60_79-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_age_60_79-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_60_79-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-depression.csv

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

  cox_ipw-cohort_vax-sub_age_60_79-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_60_79-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-self_harm.csv

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

  cox_ipw-cohort_vax-sub_age_60_79-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_60_79-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_age_80_110-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_80_110-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_age_80_110-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_80_110-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-depression.csv

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

  cox_ipw-cohort_prevax-sub_age_80_110-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_80_110-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_age_80_110-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_age_80_110-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_age_80_110-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_80_110-anxiety_general.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_age_80_110-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_80_110-depression.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-depression.csv

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

  cox_ipw-cohort_unvax-sub_age_80_110-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_80_110-self_harm.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_age_80_110-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_age_80_110-serious_mental_illness.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_age_80_110-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_80_110-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_age_80_110-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_80_110-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-depression.csv

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

  cox_ipw-cohort_vax-sub_age_80_110-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_80_110-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-self_harm.csv

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

  cox_ipw-cohort_vax-sub_age_80_110-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_age_80_110-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_covid_history-addiction:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_history-addiction.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-addiction.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-addiction.csv

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

  cox_ipw-cohort_unvax-sub_covid_history-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_history-anxiety_general.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_covid_history-anxiety_ocd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_history-anxiety_ocd.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-anxiety_ocd.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-anxiety_ocd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-anxiety_ocd.csv

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

  cox_ipw-cohort_unvax-sub_covid_history-anxiety_ptsd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_history-anxiety_ptsd.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-anxiety_ptsd.csv

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

  cox_ipw-cohort_unvax-sub_covid_history-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_history-depression.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-depression.csv

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

  cox_ipw-cohort_unvax-sub_covid_history-eating_disorders:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_history-eating_disorders.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-eating_disorders.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-eating_disorders.csv

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

  cox_ipw-cohort_unvax-sub_covid_history-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_history-self_harm.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_covid_history-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_history-serious_mental_illness.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_covid_history-suicide:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_history-suicide.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-suicide.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-suicide.csv

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

  cox_ipw-cohort_vax-sub_covid_history-addiction:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_history-addiction.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-addiction.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-addiction.csv

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

  cox_ipw-cohort_vax-sub_covid_history-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_history-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_covid_history-anxiety_ocd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_history-anxiety_ocd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-anxiety_ocd.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-anxiety_ocd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-anxiety_ocd.csv

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

  cox_ipw-cohort_vax-sub_covid_history-anxiety_ptsd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_history-anxiety_ptsd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-anxiety_ptsd.csv

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

  cox_ipw-cohort_vax-sub_covid_history-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_history-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-depression.csv

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

  cox_ipw-cohort_vax-sub_covid_history-eating_disorders:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_history-eating_disorders.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-eating_disorders.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-eating_disorders.csv

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

  cox_ipw-cohort_vax-sub_covid_history-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_history-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-self_harm.csv

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

  cox_ipw-cohort_vax-sub_covid_history-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_history-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_covid_history-suicide:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_history-suicide.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-suicide.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-suicide.csv

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-addiction:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-addiction.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-addiction.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-addiction.csv

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-anxiety_ocd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ocd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-anxiety_ocd.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ocd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-anxiety_ocd.csv

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd.csv

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-depression.csv

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-eating_disorders:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-eating_disorders.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-eating_disorders.csv

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-suicide:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-suicide.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-suicide.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-suicide.csv

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-addiction:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-addiction.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-addiction.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-addiction.csv

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-anxiety_general.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-anxiety_ocd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-anxiety_ocd.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-anxiety_ocd.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-anxiety_ocd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-anxiety_ocd.csv

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-anxiety_ptsd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-anxiety_ptsd.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-anxiety_ptsd.csv

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-depression.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-depression.csv

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-eating_disorders:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-eating_disorders.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-eating_disorders.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-eating_disorders.csv

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-self_harm.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-serious_mental_illness.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-suicide:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-suicide.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-suicide.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-suicide.csv

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-addiction:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_hospitalised-addiction.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-addiction.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-addiction.csv

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_hospitalised-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-anxiety_ocd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_hospitalised-anxiety_ocd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-anxiety_ocd.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-anxiety_ocd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-anxiety_ocd.csv

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-anxiety_ptsd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_hospitalised-anxiety_ptsd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-anxiety_ptsd.csv

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_hospitalised-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-depression.csv

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-eating_disorders:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_hospitalised-eating_disorders.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-eating_disorders.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-eating_disorders.csv

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_hospitalised-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-self_harm.csv

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_hospitalised-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-suicide:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_hospitalised-suicide.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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-suicide.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-suicide.csv

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-addiction:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-addiction.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-addiction.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-addiction.csv

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-anxiety_ocd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ocd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-anxiety_ocd.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ocd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_ocd.csv

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd.csv

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-depression.csv

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-eating_disorders:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-eating_disorders.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-eating_disorders.csv

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-suicide:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-suicide.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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-suicide.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-suicide.csv

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-addiction:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-addiction.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_nonhospitalised-addiction.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-addiction.csv

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-anxiety_general.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-anxiety_ocd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-anxiety_ocd.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_nonhospitalised-anxiety_ocd.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-anxiety_ocd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-anxiety_ocd.csv

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_nonhospitalised-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd.csv

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-depression.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-depression.csv

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-eating_disorders:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-eating_disorders.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_nonhospitalised-eating_disorders.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-eating_disorders.csv

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-self_harm.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_nonhospitalised-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-suicide:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-suicide.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_nonhospitalised-suicide.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-suicide.csv

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

  cox_ipw-cohort_vax-sub_covid_nonhospitalised-addiction:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-addiction.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_nonhospitalised-addiction.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-addiction.csv

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

  cox_ipw-cohort_vax-sub_covid_nonhospitalised-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_covid_nonhospitalised-anxiety_ocd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-anxiety_ocd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_nonhospitalised-anxiety_ocd.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-anxiety_ocd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-anxiety_ocd.csv

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

  cox_ipw-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_nonhospitalised-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd.csv

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

  cox_ipw-cohort_vax-sub_covid_nonhospitalised-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-depression.csv

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

  cox_ipw-cohort_vax-sub_covid_nonhospitalised-eating_disorders:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-eating_disorders.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_nonhospitalised-eating_disorders.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-eating_disorders.csv

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

  cox_ipw-cohort_vax-sub_covid_nonhospitalised-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_nonhospitalised-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-self_harm.csv

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

  cox_ipw-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_covid_nonhospitalised-suicide:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-suicide.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_nonhospitalised-suicide.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-suicide.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_asian-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_asian-anxiety_general.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_asian-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_asian-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_asian-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_asian-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_asian-depression.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_asian-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_asian-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_asian-depression.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_asian-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_asian-self_harm.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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_ethnicity_asian-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_asian-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_asian-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_asian-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_asian-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_asian-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_asian-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_asian-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_asian-anxiety_general.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_asian-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_asian-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_asian-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_asian-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_asian-depression.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_asian-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_asian-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_asian-depression.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_asian-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_asian-self_harm.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_ethnicity_asian-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_asian-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_asian-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_asian-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_asian-serious_mental_illness.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_asian-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_asian-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_asian-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_asian-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_asian-anxiety_general.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_asian-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_asian-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_asian-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_asian-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_asian-depression.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_asian-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_asian-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_asian-depression.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_asian-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_asian-self_harm.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_ethnicity_asian-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_asian-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_asian-self_harm.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_asian-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_asian-serious_mental_illness.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_asian-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_asian-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_asian-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_black-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_black-anxiety_general.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_black-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_black-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_black-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_black-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_black-depression.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_black-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_black-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_black-depression.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_black-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_black-self_harm.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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_ethnicity_black-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_black-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_black-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_black-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_black-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_black-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_black-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_black-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_black-anxiety_general.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_black-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_black-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_black-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_black-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_black-depression.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_black-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_black-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_black-depression.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_black-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_black-self_harm.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_ethnicity_black-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_black-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_black-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_black-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_black-serious_mental_illness.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_black-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_black-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_black-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_black-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_black-anxiety_general.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_black-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_black-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_black-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_black-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_black-depression.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_black-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_black-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_black-depression.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_black-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_black-self_harm.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_ethnicity_black-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_black-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_black-self_harm.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_black-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_black-serious_mental_illness.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_black-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_black-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_black-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_mixed-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_mixed-anxiety_general.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_mixed-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_mixed-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_mixed-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_mixed-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_mixed-depression.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_mixed-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_mixed-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_mixed-depression.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_mixed-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_mixed-self_harm.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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_ethnicity_mixed-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_mixed-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_mixed-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_mixed-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_mixed-anxiety_general.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_mixed-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_mixed-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_mixed-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_mixed-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_mixed-depression.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_mixed-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_mixed-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_mixed-depression.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_mixed-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_mixed-self_harm.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_ethnicity_mixed-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_mixed-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_mixed-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_mixed-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_mixed-serious_mental_illness.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_mixed-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_mixed-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_mixed-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_mixed-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_mixed-anxiety_general.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_mixed-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_mixed-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_mixed-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_mixed-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_mixed-depression.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_mixed-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_mixed-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_mixed-depression.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_mixed-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_mixed-self_harm.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_ethnicity_mixed-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_mixed-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_mixed-self_harm.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_mixed-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_mixed-serious_mental_illness.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_mixed-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_mixed-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_mixed-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_other-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_other-anxiety_general.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_other-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_other-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_other-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_other-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_other-depression.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_other-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_other-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_other-depression.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_other-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_other-self_harm.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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_ethnicity_other-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_other-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_other-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_other-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_other-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_other-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_other-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_other-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_other-anxiety_general.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_other-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_other-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_other-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_other-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_other-depression.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_other-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_other-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_other-depression.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_other-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_other-self_harm.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_ethnicity_other-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_other-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_other-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_other-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_other-serious_mental_illness.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_other-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_other-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_other-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_other-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_other-anxiety_general.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_other-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_other-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_other-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_other-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_other-depression.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_other-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_other-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_other-depression.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_other-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_other-self_harm.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_ethnicity_other-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_other-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_other-self_harm.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_other-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_other-serious_mental_illness.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_other-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_other-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_other-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_white-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_white-anxiety_general.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_white-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_white-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_white-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_white-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_white-depression.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_white-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_white-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_white-depression.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_white-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_white-self_harm.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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_ethnicity_white-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_white-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_white-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_ethnicity_white-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_ethnicity_white-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_ethnicity_white-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_ethnicity_white-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_white-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_white-anxiety_general.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_white-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_white-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_white-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_white-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_white-depression.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_white-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_white-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_white-depression.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_white-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_white-self_harm.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_ethnicity_white-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_white-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_white-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_ethnicity_white-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_ethnicity_white-serious_mental_illness.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_ethnicity_white-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_ethnicity_white-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_ethnicity_white-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_white-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_white-anxiety_general.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_white-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_white-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_white-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_white-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_white-depression.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_white-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_white-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_white-depression.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_white-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_white-self_harm.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_ethnicity_white-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_white-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_white-self_harm.csv

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

  cox_ipw-cohort_vax-sub_ethnicity_white-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_ethnicity_white-serious_mental_illness.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_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_white-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_ethnicity_white-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_ethnicity_white-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_priorhistory_none-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_priorhistory_none-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_none-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_priorhistory_none-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_priorhistory_none-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_priorhistory_none-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_priorhistory_none-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_none-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_priorhistory_none-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_priorhistory_none-depression.csv

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

  cox_ipw-cohort_prevax-sub_priorhistory_none-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_priorhistory_none-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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_priorhistory_none-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_priorhistory_none-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_priorhistory_none-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_priorhistory_none-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_priorhistory_none-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_none-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_priorhistory_none-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_priorhistory_none-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_priorhistory_none-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_priorhistory_none-anxiety_general.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_none-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_priorhistory_none-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_priorhistory_none-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_priorhistory_none-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_priorhistory_none-depression.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_none-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_priorhistory_none-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_priorhistory_none-depression.csv

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

  cox_ipw-cohort_unvax-sub_priorhistory_none-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_priorhistory_none-self_harm.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;
      --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_priorhistory_none-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_priorhistory_none-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_priorhistory_none-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_priorhistory_none-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_priorhistory_none-serious_mental_illness.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_none-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_priorhistory_none-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_priorhistory_none-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_priorhistory_none-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_priorhistory_none-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_none-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_priorhistory_none-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_priorhistory_none-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_priorhistory_none-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_priorhistory_none-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_none-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_priorhistory_none-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_priorhistory_none-depression.csv

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

  cox_ipw-cohort_vax-sub_priorhistory_none-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_priorhistory_none-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;
      --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_priorhistory_none-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_priorhistory_none-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_priorhistory_none-self_harm.csv

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

  cox_ipw-cohort_vax-sub_priorhistory_none-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_priorhistory_none-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_none-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_priorhistory_none-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_priorhistory_none-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_priorhistory_notrecent-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_priorhistory_notrecent-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_notrecent-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_priorhistory_notrecent-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_priorhistory_notrecent-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_priorhistory_notrecent-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_priorhistory_notrecent-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_notrecent-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_priorhistory_notrecent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_priorhistory_notrecent-depression.csv

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

  cox_ipw-cohort_prevax-sub_priorhistory_notrecent-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_priorhistory_notrecent-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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_priorhistory_notrecent-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_priorhistory_notrecent-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_priorhistory_notrecent-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_priorhistory_notrecent-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_priorhistory_notrecent-anxiety_general.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_notrecent-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_priorhistory_notrecent-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_priorhistory_notrecent-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_priorhistory_notrecent-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_priorhistory_notrecent-depression.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_notrecent-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_priorhistory_notrecent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_priorhistory_notrecent-depression.csv

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

  cox_ipw-cohort_unvax-sub_priorhistory_notrecent-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_priorhistory_notrecent-self_harm.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;
      --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_priorhistory_notrecent-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_priorhistory_notrecent-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_priorhistory_notrecent-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_priorhistory_notrecent-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_priorhistory_notrecent-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_notrecent-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_priorhistory_notrecent-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_priorhistory_notrecent-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_priorhistory_notrecent-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_priorhistory_notrecent-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_notrecent-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_priorhistory_notrecent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_priorhistory_notrecent-depression.csv

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

  cox_ipw-cohort_vax-sub_priorhistory_notrecent-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_priorhistory_notrecent-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;
      --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_priorhistory_notrecent-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_priorhistory_notrecent-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_priorhistory_notrecent-self_harm.csv

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

  cox_ipw-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_priorhistory_recent-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_priorhistory_recent-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_recent-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_priorhistory_recent-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_priorhistory_recent-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_priorhistory_recent-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_priorhistory_recent-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_recent-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_priorhistory_recent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_priorhistory_recent-depression.csv

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

  cox_ipw-cohort_prevax-sub_priorhistory_recent-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_priorhistory_recent-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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_priorhistory_recent-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_priorhistory_recent-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_priorhistory_recent-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_priorhistory_recent-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_priorhistory_recent-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_priorhistory_recent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_priorhistory_recent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_priorhistory_recent-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_priorhistory_recent-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_priorhistory_recent-anxiety_general.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_recent-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_priorhistory_recent-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_priorhistory_recent-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_priorhistory_recent-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_priorhistory_recent-depression.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_recent-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_priorhistory_recent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_priorhistory_recent-depression.csv

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

  cox_ipw-cohort_unvax-sub_priorhistory_recent-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_priorhistory_recent-self_harm.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;
      --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_priorhistory_recent-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_priorhistory_recent-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_priorhistory_recent-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_priorhistory_recent-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_priorhistory_recent-serious_mental_illness.rds
      --ipw=FALSE --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_priorhistory_recent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_priorhistory_recent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_priorhistory_recent-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_priorhistory_recent-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_priorhistory_recent-anxiety_general.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_recent-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_priorhistory_recent-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_priorhistory_recent-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_priorhistory_recent-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_priorhistory_recent-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_recent-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_priorhistory_recent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_priorhistory_recent-depression.csv

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

  cox_ipw-cohort_vax-sub_priorhistory_recent-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_priorhistory_recent-self_harm.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;
      --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_priorhistory_recent-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_priorhistory_recent-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_priorhistory_recent-self_harm.csv

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

  cox_ipw-cohort_vax-sub_priorhistory_recent-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_priorhistory_recent-serious_mental_illness.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_priorhistory_recent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_priorhistory_recent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_priorhistory_recent-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_sex_female-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_sex_female-anxiety_general.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_female-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_sex_female-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_sex_female-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_sex_female-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_sex_female-depression.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_female-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_sex_female-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_sex_female-depression.csv

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

  cox_ipw-cohort_prevax-sub_sex_female-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_sex_female-self_harm.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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_sex_female-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_sex_female-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_sex_female-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_sex_female-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_sex_female-serious_mental_illness.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_female-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_sex_female-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_sex_female-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_sex_female-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_sex_female-anxiety_general.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_sex_female-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_sex_female-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_sex_female-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_sex_female-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_sex_female-depression.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_sex_female-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_sex_female-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_sex_female-depression.csv

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

  cox_ipw-cohort_unvax-sub_sex_female-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_sex_female-self_harm.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_sex_female-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_sex_female-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_sex_female-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_sex_female-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_sex_female-serious_mental_illness.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_sex_female-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_sex_female-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_sex_female-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_sex_female-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_sex_female-anxiety_general.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_sex_female-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_sex_female-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_sex_female-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_sex_female-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_sex_female-depression.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_sex_female-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_sex_female-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_sex_female-depression.csv

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

  cox_ipw-cohort_vax-sub_sex_female-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_sex_female-self_harm.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_sex_female-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_sex_female-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_sex_female-self_harm.csv

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

  cox_ipw-cohort_vax-sub_sex_female-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_sex_female-serious_mental_illness.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_sex_female-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_sex_female-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_sex_female-serious_mental_illness.csv

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

  cox_ipw-cohort_prevax-sub_sex_male-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_sex_male-anxiety_general.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_male-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax-sub_sex_male-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_sex_male-anxiety_general.csv

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

  cox_ipw-cohort_prevax-sub_sex_male-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_sex_male-depression.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_male-depression.csv
    needs:
    - make_model_input-cohort_prevax-sub_sex_male-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_sex_male-depression.csv

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

  cox_ipw-cohort_prevax-sub_sex_male-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_sex_male-self_harm.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --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_sex_male-self_harm.csv
    needs:
    - make_model_input-cohort_prevax-sub_sex_male-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_sex_male-self_harm.csv

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

  cox_ipw-cohort_prevax-sub_sex_male-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_prevax-sub_sex_male-serious_mental_illness.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_sex_male-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax-sub_sex_male-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_sex_male-serious_mental_illness.csv

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

  cox_ipw-cohort_unvax-sub_sex_male-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_sex_male-anxiety_general.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_sex_male-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax-sub_sex_male-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_sex_male-anxiety_general.csv

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

  cox_ipw-cohort_unvax-sub_sex_male-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_sex_male-depression.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_sex_male-depression.csv
    needs:
    - make_model_input-cohort_unvax-sub_sex_male-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_sex_male-depression.csv

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

  cox_ipw-cohort_unvax-sub_sex_male-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_sex_male-self_harm.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_sex_male-self_harm.csv
    needs:
    - make_model_input-cohort_unvax-sub_sex_male-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_sex_male-self_harm.csv

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

  cox_ipw-cohort_unvax-sub_sex_male-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_unvax-sub_sex_male-serious_mental_illness.rds
      --ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_sex_male-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax-sub_sex_male-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_sex_male-serious_mental_illness.csv

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

  cox_ipw-cohort_vax-sub_sex_male-anxiety_general:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_sex_male-anxiety_general.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_sex_male-anxiety_general.csv
    needs:
    - make_model_input-cohort_vax-sub_sex_male-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_sex_male-anxiety_general.csv

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

  cox_ipw-cohort_vax-sub_sex_male-depression:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_sex_male-depression.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_sex_male-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_sex_male-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_sex_male-depression.csv

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

  cox_ipw-cohort_vax-sub_sex_male-self_harm:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_sex_male-self_harm.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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_sex_male-self_harm.csv
    needs:
    - make_model_input-cohort_vax-sub_sex_male-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_sex_male-self_harm.csv

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

  cox_ipw-cohort_vax-sub_sex_male-serious_mental_illness:
    run: cox-ipw:v0.0.17 --df_input=model_input-cohort_vax-sub_sex_male-serious_mental_illness.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
      --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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --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=10 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_sex_male-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_sex_male-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_sex_male-serious_mental_illness.csv

  ## Stage 6 - make model output 

  make_model_output:
    run: r:latest analysis/model/make_model_output.R
    needs:
    - cox_ipw-cohort_prevax-main-addiction
    - cox_ipw-cohort_prevax-sub_covid_hospitalised-addiction
    - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-addiction
    - cox_ipw-cohort_vax-main-addiction
    - cox_ipw-cohort_vax-sub_covid_hospitalised-addiction
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-addiction
    - cox_ipw-cohort_vax-sub_covid_history-addiction
    - cox_ipw-cohort_unvax-main-addiction
    - cox_ipw-cohort_unvax-sub_covid_hospitalised-addiction
    - cox_ipw-cohort_unvax-sub_covid_nonhospitalised-addiction
    - cox_ipw-cohort_unvax-sub_covid_history-addiction
    - cox_ipw-cohort_prevax-main-anxiety_general
    - cox_ipw-cohort_prevax-sub_covid_hospitalised-anxiety_general
    - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-anxiety_general
    - cox_ipw-cohort_prevax-sub_priorhistory_none-anxiety_general
    - cox_ipw-cohort_prevax-sub_priorhistory_recent-anxiety_general
    - cox_ipw-cohort_prevax-sub_priorhistory_notrecent-anxiety_general
    - cox_ipw-cohort_prevax-sub_sex_female-anxiety_general
    - cox_ipw-cohort_prevax-sub_sex_male-anxiety_general
    - cox_ipw-cohort_prevax-sub_age_18_39-anxiety_general
    - cox_ipw-cohort_prevax-sub_age_40_59-anxiety_general
    - cox_ipw-cohort_prevax-sub_age_60_79-anxiety_general
    - cox_ipw-cohort_prevax-sub_age_80_110-anxiety_general
    - cox_ipw-cohort_prevax-sub_ethnicity_white-anxiety_general
    - cox_ipw-cohort_prevax-sub_ethnicity_black-anxiety_general
    - cox_ipw-cohort_prevax-sub_ethnicity_mixed-anxiety_general
    - cox_ipw-cohort_prevax-sub_ethnicity_asian-anxiety_general
    - cox_ipw-cohort_prevax-sub_ethnicity_other-anxiety_general
    - cox_ipw-cohort_vax-main-anxiety_general
    - cox_ipw-cohort_vax-sub_covid_hospitalised-anxiety_general
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-anxiety_general
    - cox_ipw-cohort_vax-sub_covid_history-anxiety_general
    - cox_ipw-cohort_vax-sub_priorhistory_none-anxiety_general
    - cox_ipw-cohort_vax-sub_priorhistory_recent-anxiety_general
    - cox_ipw-cohort_vax-sub_priorhistory_notrecent-anxiety_general
    - cox_ipw-cohort_vax-sub_sex_female-anxiety_general
    - cox_ipw-cohort_vax-sub_sex_male-anxiety_general
    - cox_ipw-cohort_vax-sub_age_18_39-anxiety_general
    - cox_ipw-cohort_vax-sub_age_40_59-anxiety_general
    - cox_ipw-cohort_vax-sub_age_60_79-anxiety_general
    - cox_ipw-cohort_vax-sub_age_80_110-anxiety_general
    - cox_ipw-cohort_vax-sub_ethnicity_white-anxiety_general
    - cox_ipw-cohort_vax-sub_ethnicity_black-anxiety_general
    - cox_ipw-cohort_vax-sub_ethnicity_mixed-anxiety_general
    - cox_ipw-cohort_vax-sub_ethnicity_asian-anxiety_general
    - cox_ipw-cohort_vax-sub_ethnicity_other-anxiety_general
    - cox_ipw-cohort_unvax-main-anxiety_general
    - cox_ipw-cohort_unvax-sub_covid_hospitalised-anxiety_general
    - cox_ipw-cohort_unvax-sub_covid_nonhospitalised-anxiety_general
    - cox_ipw-cohort_unvax-sub_covid_history-anxiety_general
    - cox_ipw-cohort_unvax-sub_priorhistory_none-anxiety_general
    - cox_ipw-cohort_unvax-sub_priorhistory_recent-anxiety_general
    - cox_ipw-cohort_unvax-sub_priorhistory_notrecent-anxiety_general
    - cox_ipw-cohort_unvax-sub_sex_female-anxiety_general
    - cox_ipw-cohort_unvax-sub_sex_male-anxiety_general
    - cox_ipw-cohort_unvax-sub_age_18_39-anxiety_general
    - cox_ipw-cohort_unvax-sub_age_40_59-anxiety_general
    - cox_ipw-cohort_unvax-sub_age_60_79-anxiety_general
    - cox_ipw-cohort_unvax-sub_age_80_110-anxiety_general
    - cox_ipw-cohort_unvax-sub_ethnicity_white-anxiety_general
    - cox_ipw-cohort_unvax-sub_ethnicity_black-anxiety_general
    - cox_ipw-cohort_unvax-sub_ethnicity_mixed-anxiety_general
    - cox_ipw-cohort_unvax-sub_ethnicity_asian-anxiety_general
    - cox_ipw-cohort_unvax-sub_ethnicity_other-anxiety_general
    - cox_ipw-cohort_prevax-main-anxiety_ptsd
    - cox_ipw-cohort_prevax-sub_covid_hospitalised-anxiety_ptsd
    - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-anxiety_ptsd
    - cox_ipw-cohort_vax-main-anxiety_ptsd
    - cox_ipw-cohort_vax-sub_covid_hospitalised-anxiety_ptsd
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd
    - cox_ipw-cohort_vax-sub_covid_history-anxiety_ptsd
    - cox_ipw-cohort_unvax-main-anxiety_ptsd
    - cox_ipw-cohort_unvax-sub_covid_hospitalised-anxiety_ptsd
    - cox_ipw-cohort_unvax-sub_covid_nonhospitalised-anxiety_ptsd
    - cox_ipw-cohort_unvax-sub_covid_history-anxiety_ptsd
    - cox_ipw-cohort_prevax-main-depression
    - cox_ipw-cohort_prevax-sub_covid_hospitalised-depression
    - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-depression
    - cox_ipw-cohort_prevax-sub_priorhistory_none-depression
    - cox_ipw-cohort_prevax-sub_priorhistory_recent-depression
    - cox_ipw-cohort_prevax-sub_priorhistory_notrecent-depression
    - cox_ipw-cohort_prevax-sub_sex_female-depression
    - cox_ipw-cohort_prevax-sub_sex_male-depression
    - cox_ipw-cohort_prevax-sub_age_18_39-depression
    - cox_ipw-cohort_prevax-sub_age_40_59-depression
    - cox_ipw-cohort_prevax-sub_age_60_79-depression
    - cox_ipw-cohort_prevax-sub_age_80_110-depression
    - cox_ipw-cohort_prevax-sub_ethnicity_white-depression
    - cox_ipw-cohort_prevax-sub_ethnicity_black-depression
    - cox_ipw-cohort_prevax-sub_ethnicity_mixed-depression
    - cox_ipw-cohort_prevax-sub_ethnicity_asian-depression
    - cox_ipw-cohort_prevax-sub_ethnicity_other-depression
    - cox_ipw-cohort_vax-main-depression
    - cox_ipw-cohort_vax-sub_covid_hospitalised-depression
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-depression
    - cox_ipw-cohort_vax-sub_covid_history-depression
    - cox_ipw-cohort_vax-sub_priorhistory_none-depression
    - cox_ipw-cohort_vax-sub_priorhistory_recent-depression
    - cox_ipw-cohort_vax-sub_priorhistory_notrecent-depression
    - cox_ipw-cohort_vax-sub_sex_female-depression
    - cox_ipw-cohort_vax-sub_sex_male-depression
    - cox_ipw-cohort_vax-sub_age_18_39-depression
    - cox_ipw-cohort_vax-sub_age_40_59-depression
    - cox_ipw-cohort_vax-sub_age_60_79-depression
    - cox_ipw-cohort_vax-sub_age_80_110-depression
    - cox_ipw-cohort_vax-sub_ethnicity_white-depression
    - cox_ipw-cohort_vax-sub_ethnicity_black-depression
    - cox_ipw-cohort_vax-sub_ethnicity_mixed-depression
    - cox_ipw-cohort_vax-sub_ethnicity_asian-depression
    - cox_ipw-cohort_vax-sub_ethnicity_other-depression
    - cox_ipw-cohort_unvax-main-depression
    - cox_ipw-cohort_unvax-sub_covid_hospitalised-depression
    - cox_ipw-cohort_unvax-sub_covid_nonhospitalised-depression
    - cox_ipw-cohort_unvax-sub_covid_history-depression
    - cox_ipw-cohort_unvax-sub_priorhistory_none-depression
    - cox_ipw-cohort_unvax-sub_priorhistory_recent-depression
    - cox_ipw-cohort_unvax-sub_priorhistory_notrecent-depression
    - cox_ipw-cohort_unvax-sub_sex_female-depression
    - cox_ipw-cohort_unvax-sub_sex_male-depression
    - cox_ipw-cohort_unvax-sub_age_18_39-depression
    - cox_ipw-cohort_unvax-sub_age_40_59-depression
    - cox_ipw-cohort_unvax-sub_age_60_79-depression
    - cox_ipw-cohort_unvax-sub_age_80_110-depression
    - cox_ipw-cohort_unvax-sub_ethnicity_white-depression
    - cox_ipw-cohort_unvax-sub_ethnicity_black-depression
    - cox_ipw-cohort_unvax-sub_ethnicity_mixed-depression
    - cox_ipw-cohort_unvax-sub_ethnicity_asian-depression
    - cox_ipw-cohort_unvax-sub_ethnicity_other-depression
    - cox_ipw-cohort_prevax-main-eating_disorders
    - cox_ipw-cohort_prevax-sub_covid_hospitalised-eating_disorders
    - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-eating_disorders
    - cox_ipw-cohort_prevax-main-self_harm
    - cox_ipw-cohort_prevax-sub_covid_hospitalised-self_harm
    - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-self_harm
    - cox_ipw-cohort_prevax-sub_sex_female-self_harm
    - cox_ipw-cohort_prevax-sub_sex_male-self_harm
    - cox_ipw-cohort_prevax-sub_age_18_39-self_harm
    - cox_ipw-cohort_prevax-sub_age_40_59-self_harm
    - cox_ipw-cohort_prevax-sub_age_60_79-self_harm
    - cox_ipw-cohort_prevax-sub_age_80_110-self_harm
    - cox_ipw-cohort_prevax-sub_ethnicity_white-self_harm
    - cox_ipw-cohort_prevax-sub_ethnicity_black-self_harm
    - cox_ipw-cohort_prevax-sub_ethnicity_mixed-self_harm
    - cox_ipw-cohort_prevax-sub_ethnicity_asian-self_harm
    - cox_ipw-cohort_prevax-sub_ethnicity_other-self_harm
    - cox_ipw-cohort_vax-main-self_harm
    - cox_ipw-cohort_vax-sub_covid_hospitalised-self_harm
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-self_harm
    - cox_ipw-cohort_vax-sub_covid_history-self_harm
    - cox_ipw-cohort_vax-sub_priorhistory_recent-self_harm
    - cox_ipw-cohort_vax-sub_sex_female-self_harm
    - cox_ipw-cohort_vax-sub_sex_male-self_harm
    - cox_ipw-cohort_vax-sub_age_18_39-self_harm
    - cox_ipw-cohort_vax-sub_age_40_59-self_harm
    - cox_ipw-cohort_vax-sub_age_60_79-self_harm
    - cox_ipw-cohort_vax-sub_age_80_110-self_harm
    - cox_ipw-cohort_vax-sub_ethnicity_white-self_harm
    - cox_ipw-cohort_vax-sub_ethnicity_black-self_harm
    - cox_ipw-cohort_vax-sub_ethnicity_mixed-self_harm
    - cox_ipw-cohort_vax-sub_ethnicity_asian-self_harm
    - cox_ipw-cohort_vax-sub_ethnicity_other-self_harm
    - cox_ipw-cohort_unvax-main-self_harm
    - cox_ipw-cohort_unvax-sub_covid_hospitalised-self_harm
    - cox_ipw-cohort_unvax-sub_covid_nonhospitalised-self_harm
    - cox_ipw-cohort_unvax-sub_covid_history-self_harm
    - cox_ipw-cohort_unvax-sub_priorhistory_recent-self_harm
    - cox_ipw-cohort_unvax-sub_sex_female-self_harm
    - cox_ipw-cohort_unvax-sub_sex_male-self_harm
    - cox_ipw-cohort_unvax-sub_age_18_39-self_harm
    - cox_ipw-cohort_unvax-sub_age_40_59-self_harm
    - cox_ipw-cohort_unvax-sub_age_60_79-self_harm
    - cox_ipw-cohort_unvax-sub_age_80_110-self_harm
    - cox_ipw-cohort_unvax-sub_ethnicity_white-self_harm
    - cox_ipw-cohort_unvax-sub_ethnicity_black-self_harm
    - cox_ipw-cohort_unvax-sub_ethnicity_mixed-self_harm
    - cox_ipw-cohort_unvax-sub_ethnicity_asian-self_harm
    - cox_ipw-cohort_unvax-sub_ethnicity_other-self_harm
    - cox_ipw-cohort_prevax-main-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_covid_hospitalised-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_priorhistory_none-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_priorhistory_recent-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_priorhistory_notrecent-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_sex_female-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_sex_male-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_age_18_39-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_age_40_59-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_age_60_79-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_age_80_110-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_ethnicity_white-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_ethnicity_black-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_ethnicity_mixed-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_ethnicity_asian-serious_mental_illness
    - cox_ipw-cohort_prevax-sub_ethnicity_other-serious_mental_illness
    - cox_ipw-cohort_vax-main-serious_mental_illness
    - cox_ipw-cohort_vax-sub_covid_hospitalised-serious_mental_illness
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness
    - cox_ipw-cohort_vax-sub_covid_history-serious_mental_illness
    - cox_ipw-cohort_vax-sub_priorhistory_none-serious_mental_illness
    - cox_ipw-cohort_vax-sub_priorhistory_recent-serious_mental_illness
    - cox_ipw-cohort_vax-sub_priorhistory_notrecent-serious_mental_illness
    - cox_ipw-cohort_vax-sub_sex_female-serious_mental_illness
    - cox_ipw-cohort_vax-sub_sex_male-serious_mental_illness
    - cox_ipw-cohort_vax-sub_age_18_39-serious_mental_illness
    - cox_ipw-cohort_vax-sub_age_40_59-serious_mental_illness
    - cox_ipw-cohort_vax-sub_age_60_79-serious_mental_illness
    - cox_ipw-cohort_vax-sub_age_80_110-serious_mental_illness
    - cox_ipw-cohort_vax-sub_ethnicity_white-serious_mental_illness
    - cox_ipw-cohort_vax-sub_ethnicity_black-serious_mental_illness
    - cox_ipw-cohort_vax-sub_ethnicity_mixed-serious_mental_illness
    - cox_ipw-cohort_vax-sub_ethnicity_asian-serious_mental_illness
    - cox_ipw-cohort_vax-sub_ethnicity_other-serious_mental_illness
    - cox_ipw-cohort_unvax-main-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_covid_hospitalised-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_covid_nonhospitalised-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_covid_history-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_priorhistory_none-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_priorhistory_recent-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_priorhistory_notrecent-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_sex_female-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_sex_male-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_age_18_39-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_age_40_59-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_age_60_79-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_age_80_110-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_ethnicity_white-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_ethnicity_black-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_ethnicity_mixed-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_ethnicity_asian-serious_mental_illness
    - cox_ipw-cohort_unvax-sub_ethnicity_other-serious_mental_illness
    - cox_ipw-cohort_prevax-main-suicide
    - cox_ipw-cohort_prevax-sub_covid_hospitalised-suicide
    - cox_ipw-cohort_prevax-sub_covid_nonhospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output.csv

  ## Temp 

  cox_ipw-cohort_prevax-main-depression-v0.0.9:
    run: cox-ipw:v0.0.9 --df_input=model_input-cohort_prevax-main-depression.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_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_priorhistory_depression;cov_cat_priorhistory_anxiety_general;cov_cat_priorhistory_eating_disorders;cov_cat_priorhistory_serious_mental_illness;cov_cat_priorhistory_self_harm
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --