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.gz
        vax_eligible_dates: output/vax_eligible_dates.csv.gz

  ## Generate prelim study_definition 

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

  ## Generate 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.gz

  ## Generate study population - prevax_extf 

  generate_study_population_prevax_extf:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax_extf
      --output-format csv.gz
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_prevax_extf.csv.gz

  ## Generate study population - unvax_extf 

  generate_study_population_unvax_extf:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax_extf
      --output-format csv.gz
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_unvax_extf.csv.gz

  ## Generate study population - vax 

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

  ## Preprocess data - prevax_extf 

  preprocess_data_prevax_extf:
    run: r:latest analysis/preprocess_data.R prevax_extf
    needs:
    - generate_index_dates
    - generate_study_population_prevax_extf
    outputs:
      moderately_sensitive:
        describe: output/describe_input_prevax_extf_stage0.txt
        describe_venn: output/describe_venn_prevax_extf.txt
      highly_sensitive:
        cohort: output/input_prevax_extf.rds
        venn: output/venn_prevax_extf.rds

  ## Preprocess data - unvax_extf 

  preprocess_data_unvax_extf:
    run: r:latest analysis/preprocess_data.R unvax_extf
    needs:
    - generate_index_dates
    - generate_study_population_unvax_extf
    outputs:
      moderately_sensitive:
        describe: output/describe_input_unvax_extf_stage0.txt
        describe_venn: output/describe_venn_unvax_extf.txt
      highly_sensitive:
        cohort: output/input_unvax_extf.rds
        venn: output/venn_unvax_extf.rds

  ## Preprocess data - vax 

  preprocess_data_vax:
    run: r:latest analysis/preprocess_data.R vax
    needs:
    - generate_index_dates
    - generate_study_population_vax
    outputs:
      moderately_sensitive:
        describe: output/describe_input_vax_stage0.txt
        describe_venn: output/describe_venn_vax.txt
      highly_sensitive:
        cohort: output/input_vax.rds
        venn: output/venn_vax.rds

  ## Stage 1 - data cleaning - prevax_extf 

  stage1_data_cleaning_prevax_extf:
    run: r:latest analysis/stage1_data_cleaning.R prevax_extf
    needs:
    - vax_eligibility_inputs
    - preprocess_data_prevax_extf
    outputs:
      moderately_sensitive:
        consort: output/consort_prevax_extf.csv
        consort_rounded: output/consort_prevax_extf_rounded.csv
      highly_sensitive:
        cohort: output/input_prevax_extf_stage1.rds

  describe_stage1_data_cleaning_prevax_extf:
    run: r:latest analysis/describe_file.R input_prevax_extf_stage1 rds
    needs:
    - stage1_data_cleaning_prevax_extf
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_prevax_extf_stage1.txt

  ## Stage 1 - data cleaning - unvax_extf 

  stage1_data_cleaning_unvax_extf:
    run: r:latest analysis/stage1_data_cleaning.R unvax_extf
    needs:
    - vax_eligibility_inputs
    - preprocess_data_unvax_extf
    outputs:
      moderately_sensitive:
        consort: output/consort_unvax_extf.csv
        consort_rounded: output/consort_unvax_extf_rounded.csv
      highly_sensitive:
        cohort: output/input_unvax_extf_stage1.rds

  describe_stage1_data_cleaning_unvax_extf:
    run: r:latest analysis/describe_file.R input_unvax_extf_stage1 rds
    needs:
    - stage1_data_cleaning_unvax_extf
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_unvax_extf_stage1.txt

  ## Stage 1 - data cleaning - vax 

  stage1_data_cleaning_vax:
    run: r:latest analysis/stage1_data_cleaning.R vax
    needs:
    - vax_eligibility_inputs
    - preprocess_data_vax
    outputs:
      moderately_sensitive:
        consort: output/consort_vax.csv
        consort_rounded: output/consort_vax_rounded.csv
      highly_sensitive:
        cohort: output/input_vax_stage1.rds

  describe_stage1_data_cleaning_vax:
    run: r:latest analysis/describe_file.R input_vax_stage1 rds
    needs:
    - stage1_data_cleaning_vax
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_vax_stage1.txt

  ## Table 1 - prevax_extf 

  table1_prevax_extf:
    run: r:latest analysis/table1.R prevax_extf
    needs:
    - stage1_data_cleaning_prevax_extf
    outputs:
      moderately_sensitive:
        table1: output/table1_prevax_extf.csv
        table1_rounded: output/table1_prevax_extf_rounded.csv

  extendedtable1_prevax_extf:
    run: r:latest analysis/extendedtable1.R prevax_extf
    needs:
    - stage1_data_cleaning_prevax_extf
    outputs:
      moderately_sensitive:
        extendedtable1: output/extendedtable1_prevax_extf.csv
        extendedtable1_rounded: output/extendedtable1_prevax_extf_rounded.csv

  ## Table 1 - unvax_extf 

  table1_unvax_extf:
    run: r:latest analysis/table1.R unvax_extf
    needs:
    - stage1_data_cleaning_unvax_extf
    outputs:
      moderately_sensitive:
        table1: output/table1_unvax_extf.csv
        table1_rounded: output/table1_unvax_extf_rounded.csv

  extendedtable1_unvax_extf:
    run: r:latest analysis/extendedtable1.R unvax_extf
    needs:
    - stage1_data_cleaning_unvax_extf
    outputs:
      moderately_sensitive:
        extendedtable1: output/extendedtable1_unvax_extf.csv
        extendedtable1_rounded: output/extendedtable1_unvax_extf_rounded.csv

  ## Table 1 - vax 

  table1_vax:
    run: r:latest analysis/table1.R vax
    needs:
    - stage1_data_cleaning_vax
    outputs:
      moderately_sensitive:
        table1: output/table1_vax.csv
        table1_rounded: output/table1_vax_rounded.csv

  extendedtable1_vax:
    run: r:latest analysis/extendedtable1.R vax
    needs:
    - stage1_data_cleaning_vax
    outputs:
      moderately_sensitive:
        extendedtable1: output/extendedtable1_vax.csv
        extendedtable1_rounded: output/extendedtable1_vax_rounded.csv

  ## Replace suicide variable with data from death registry only 

  replace_suicide:
    run: r:latest analysis/replace_suicide.R
    needs:
    - preprocess_data_prevax_extf
    - preprocess_data_vax
    - preprocess_data_unvax_extf
    - stage1_data_cleaning_prevax_extf
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax_extf
    outputs:
      highly_sensitive:
        prevax_cohort: output/input_prevax_extf_stage1_v1.rds
        vax_cohort: output/input_vax_stage1_v1.rds
        unvax_cohort: output/input_unvax_extf_stage1_v1.rds

  ## Run models 

  make_model_input-cohort_prevax_extf-day0_main-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_main-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_main-depression.rds

  cox_ipw-cohort_prevax_extf-day0_main-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=10
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_main-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_main-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_main-depression.csv

  make_model_input-cohort_prevax_extf-day0_main-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_main-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_main-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-day0_main-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=10
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_main-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_main-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_main-serious_mental_illness.csv

  make_model_input-cohort_prevax_extf-day0_main-suicide:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_main-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_main-suicide.rds

  cox_ipw-cohort_prevax_extf-day0_main-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_main-suicide.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_main-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_main-suicide.csv

  make_model_input-cohort_unvax_extf-day0_main-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_main-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_main-depression.rds

  cox_ipw-cohort_unvax_extf-day0_main-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_main-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_main-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_main-depression.csv

  make_model_input-cohort_unvax_extf-day0_main-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_main-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_main-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-day0_main-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_main-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_main-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_main-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-day0_main-suicide:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_main-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_main-suicide.rds

  cox_ipw-cohort_unvax_extf-day0_main-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_main-suicide.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_main-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_main-suicide.csv

  make_model_input-cohort_vax-day0_main-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_main-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_main-depression.rds

  cox_ipw-cohort_vax-day0_main-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_main-depression.csv
    needs:
    - make_model_input-cohort_vax-day0_main-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_main-depression.csv

  make_model_input-cohort_vax-day0_main-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_main-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_main-serious_mental_illness.rds

  cox_ipw-cohort_vax-day0_main-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_main-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-day0_main-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_main-serious_mental_illness.csv

  make_model_input-cohort_vax-day0_main-suicide:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_main-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_main-suicide.rds

  cox_ipw-cohort_vax-day0_main-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_main-suicide.csv
    needs:
    - make_model_input-cohort_vax-day0_main-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_main-suicide.csv

  make_model_input-cohort_prevax_extf-day0_sub_covid_hospitalised-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_sub_covid_hospitalised-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_sub_covid_hospitalised-depression.rds

  cox_ipw-cohort_prevax_extf-day0_sub_covid_hospitalised-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=10
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_sub_covid_hospitalised-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_sub_covid_hospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_sub_covid_hospitalised-depression.csv

  make_model_input-cohort_prevax_extf-day0_sub_covid_hospitalised-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_sub_covid_hospitalised-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_sub_covid_hospitalised-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-day0_sub_covid_hospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=10
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_sub_covid_hospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_sub_covid_hospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_sub_covid_hospitalised-serious_mental_illness.csv

  make_model_input-cohort_prevax_extf-day0_sub_covid_hospitalised-suicide:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_sub_covid_hospitalised-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_sub_covid_hospitalised-suicide.rds

  cox_ipw-cohort_prevax_extf-day0_sub_covid_hospitalised-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_sub_covid_hospitalised-suicide.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_sub_covid_hospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_sub_covid_hospitalised-suicide.csv

  make_model_input-cohort_unvax_extf-day0_sub_covid_hospitalised-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_sub_covid_hospitalised-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_sub_covid_hospitalised-depression.rds

  cox_ipw-cohort_unvax_extf-day0_sub_covid_hospitalised-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_sub_covid_hospitalised-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_sub_covid_hospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_sub_covid_hospitalised-depression.csv

  make_model_input-cohort_unvax_extf-day0_sub_covid_hospitalised-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_sub_covid_hospitalised-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_sub_covid_hospitalised-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-day0_sub_covid_hospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_sub_covid_hospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_sub_covid_hospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_sub_covid_hospitalised-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-day0_sub_covid_hospitalised-suicide:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_sub_covid_hospitalised-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_sub_covid_hospitalised-suicide.rds

  cox_ipw-cohort_unvax_extf-day0_sub_covid_hospitalised-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_sub_covid_hospitalised-suicide.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_sub_covid_hospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_sub_covid_hospitalised-suicide.csv

  make_model_input-cohort_vax-day0_sub_covid_hospitalised-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_sub_covid_hospitalised-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_sub_covid_hospitalised-depression.rds

  cox_ipw-cohort_vax-day0_sub_covid_hospitalised-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_sub_covid_hospitalised-depression.csv
    needs:
    - make_model_input-cohort_vax-day0_sub_covid_hospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_sub_covid_hospitalised-depression.csv

  make_model_input-cohort_vax-day0_sub_covid_hospitalised-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_sub_covid_hospitalised-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_sub_covid_hospitalised-serious_mental_illness.rds

  cox_ipw-cohort_vax-day0_sub_covid_hospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_sub_covid_hospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-day0_sub_covid_hospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_sub_covid_hospitalised-serious_mental_illness.csv

  make_model_input-cohort_vax-day0_sub_covid_hospitalised-suicide:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_sub_covid_hospitalised-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_sub_covid_hospitalised-suicide.rds

  cox_ipw-cohort_vax-day0_sub_covid_hospitalised-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_sub_covid_hospitalised-suicide.csv
    needs:
    - make_model_input-cohort_vax-day0_sub_covid_hospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_sub_covid_hospitalised-suicide.csv

  make_model_input-cohort_prevax_extf-day0_sub_covid_nonhospitalised-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_sub_covid_nonhospitalised-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_sub_covid_nonhospitalised-depression.rds

  cox_ipw-cohort_prevax_extf-day0_sub_covid_nonhospitalised-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=10
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_sub_covid_nonhospitalised-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_sub_covid_nonhospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_sub_covid_nonhospitalised-depression.csv

  make_model_input-cohort_prevax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=10
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness.csv

  make_model_input-cohort_prevax_extf-day0_sub_covid_nonhospitalised-suicide:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_sub_covid_nonhospitalised-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_sub_covid_nonhospitalised-suicide.rds

  cox_ipw-cohort_prevax_extf-day0_sub_covid_nonhospitalised-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_sub_covid_nonhospitalised-suicide.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_sub_covid_nonhospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_sub_covid_nonhospitalised-suicide.csv

  make_model_input-cohort_unvax_extf-day0_sub_covid_nonhospitalised-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_sub_covid_nonhospitalised-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_sub_covid_nonhospitalised-depression.rds

  cox_ipw-cohort_unvax_extf-day0_sub_covid_nonhospitalised-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_sub_covid_nonhospitalised-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_sub_covid_nonhospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_sub_covid_nonhospitalised-depression.csv

  make_model_input-cohort_unvax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_sub_covid_nonhospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-day0_sub_covid_nonhospitalised-suicide:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_sub_covid_nonhospitalised-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_sub_covid_nonhospitalised-suicide.rds

  cox_ipw-cohort_unvax_extf-day0_sub_covid_nonhospitalised-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_sub_covid_nonhospitalised-suicide.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_sub_covid_nonhospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_sub_covid_nonhospitalised-suicide.csv

  make_model_input-cohort_vax-day0_sub_covid_nonhospitalised-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_sub_covid_nonhospitalised-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_sub_covid_nonhospitalised-depression.rds

  cox_ipw-cohort_vax-day0_sub_covid_nonhospitalised-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_sub_covid_nonhospitalised-depression.csv
    needs:
    - make_model_input-cohort_vax-day0_sub_covid_nonhospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_sub_covid_nonhospitalised-depression.csv

  make_model_input-cohort_vax-day0_sub_covid_nonhospitalised-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_sub_covid_nonhospitalised-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_sub_covid_nonhospitalised-serious_mental_illness.rds

  cox_ipw-cohort_vax-day0_sub_covid_nonhospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_sub_covid_nonhospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-day0_sub_covid_nonhospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_sub_covid_nonhospitalised-serious_mental_illness.csv

  make_model_input-cohort_vax-day0_sub_covid_nonhospitalised-suicide:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_sub_covid_nonhospitalised-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_sub_covid_nonhospitalised-suicide.rds

  cox_ipw-cohort_vax-day0_sub_covid_nonhospitalised-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_sub_covid_nonhospitalised-suicide.csv
    needs:
    - make_model_input-cohort_vax-day0_sub_covid_nonhospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_sub_covid_nonhospitalised-suicide.csv

  make_model_input-cohort_prevax_extf-day0_sub_history_none-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_sub_history_none-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_sub_history_none-depression.rds

  cox_ipw-cohort_prevax_extf-day0_sub_history_none-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=10
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_sub_history_none-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_sub_history_none-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_sub_history_none-depression.csv

  make_model_input-cohort_prevax_extf-day0_sub_history_none-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_sub_history_none-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_sub_history_none-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-day0_sub_history_none-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=10
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_sub_history_none-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_sub_history_none-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_sub_history_none-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-day0_sub_history_none-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_sub_history_none-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_sub_history_none-depression.rds

  cox_ipw-cohort_unvax_extf-day0_sub_history_none-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_sub_history_none-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_sub_history_none-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_sub_history_none-depression.csv

  make_model_input-cohort_unvax_extf-day0_sub_history_none-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_sub_history_none-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_sub_history_none-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-day0_sub_history_none-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_sub_history_none-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_sub_history_none-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_sub_history_none-serious_mental_illness.csv

  make_model_input-cohort_vax-day0_sub_history_none-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_sub_history_none-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_sub_history_none-depression.rds

  cox_ipw-cohort_vax-day0_sub_history_none-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_sub_history_none-depression.csv
    needs:
    - make_model_input-cohort_vax-day0_sub_history_none-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_sub_history_none-depression.csv

  make_model_input-cohort_vax-day0_sub_history_none-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_sub_history_none-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_sub_history_none-serious_mental_illness.rds

  cox_ipw-cohort_vax-day0_sub_history_none-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_sub_history_none-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-day0_sub_history_none-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_sub_history_none-serious_mental_illness.csv

  make_model_input-cohort_prevax_extf-day0_sub_history_notrecent-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_sub_history_notrecent-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_sub_history_notrecent-depression.rds

  cox_ipw-cohort_prevax_extf-day0_sub_history_notrecent-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=10
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_sub_history_notrecent-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_sub_history_notrecent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_sub_history_notrecent-depression.csv

  make_model_input-cohort_prevax_extf-day0_sub_history_notrecent-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_sub_history_notrecent-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_sub_history_notrecent-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-day0_sub_history_notrecent-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=10
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_sub_history_notrecent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_sub_history_notrecent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_sub_history_notrecent-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-day0_sub_history_notrecent-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_sub_history_notrecent-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_sub_history_notrecent-depression.rds

  cox_ipw-cohort_unvax_extf-day0_sub_history_notrecent-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_sub_history_notrecent-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_sub_history_notrecent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_sub_history_notrecent-depression.csv

  make_model_input-cohort_unvax_extf-day0_sub_history_notrecent-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_sub_history_notrecent-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_sub_history_notrecent-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-day0_sub_history_notrecent-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_sub_history_notrecent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_sub_history_notrecent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_sub_history_notrecent-serious_mental_illness.csv

  make_model_input-cohort_vax-day0_sub_history_notrecent-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_sub_history_notrecent-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_sub_history_notrecent-depression.rds

  cox_ipw-cohort_vax-day0_sub_history_notrecent-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_sub_history_notrecent-depression.csv
    needs:
    - make_model_input-cohort_vax-day0_sub_history_notrecent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_sub_history_notrecent-depression.csv

  make_model_input-cohort_vax-day0_sub_history_notrecent-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_sub_history_notrecent-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_sub_history_notrecent-serious_mental_illness.rds

  cox_ipw-cohort_vax-day0_sub_history_notrecent-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_sub_history_notrecent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-day0_sub_history_notrecent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_sub_history_notrecent-serious_mental_illness.csv

  make_model_input-cohort_prevax_extf-day0_sub_history_recent-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_sub_history_recent-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_sub_history_recent-depression.rds

  cox_ipw-cohort_prevax_extf-day0_sub_history_recent-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=10
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_sub_history_recent-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_sub_history_recent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_sub_history_recent-depression.csv

  make_model_input-cohort_prevax_extf-day0_sub_history_recent-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-day0_sub_history_recent-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-day0_sub_history_recent-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-day0_sub_history_recent-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-day0_sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=10
      --total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
      --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-day0_sub_history_recent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-day0_sub_history_recent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-day0_sub_history_recent-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-day0_sub_history_recent-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_sub_history_recent-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_sub_history_recent-depression.rds

  cox_ipw-cohort_unvax_extf-day0_sub_history_recent-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_sub_history_recent-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_sub_history_recent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_sub_history_recent-depression.csv

  make_model_input-cohort_unvax_extf-day0_sub_history_recent-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-day0_sub_history_recent-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-day0_sub_history_recent-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-day0_sub_history_recent-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-day0_sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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_extf-day0_sub_history_recent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-day0_sub_history_recent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-day0_sub_history_recent-serious_mental_illness.csv

  make_model_input-cohort_vax-day0_sub_history_recent-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_sub_history_recent-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_sub_history_recent-depression.rds

  cox_ipw-cohort_vax-day0_sub_history_recent-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_sub_history_recent-depression.csv
    needs:
    - make_model_input-cohort_vax-day0_sub_history_recent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_sub_history_recent-depression.csv

  make_model_input-cohort_vax-day0_sub_history_recent-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-day0_sub_history_recent-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-day0_sub_history_recent-serious_mental_illness.rds

  cox_ipw-cohort_vax-day0_sub_history_recent-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-day0_sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=1;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-day0_sub_history_recent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-day0_sub_history_recent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-day0_sub_history_recent-serious_mental_illness.csv

  make_model_input-cohort_prevax_extf-main-addiction:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-addiction
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-main-addiction.rds

  cox_ipw-cohort_prevax_extf-main-addiction:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-addiction.csv
    needs:
    - make_model_input-cohort_prevax_extf-main-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-main-addiction.csv

  make_model_input-cohort_prevax_extf-main-anxiety_general:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-anxiety_general
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-main-anxiety_general.rds

  cox_ipw-cohort_prevax_extf-main-anxiety_general:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax_extf-main-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-main-anxiety_general.csv

  make_model_input-cohort_prevax_extf-main-anxiety_ptsd:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-anxiety_ptsd
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-main-anxiety_ptsd.rds

  cox_ipw-cohort_prevax_extf-main-anxiety_ptsd:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_prevax_extf-main-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-main-anxiety_ptsd.csv

  make_model_input-cohort_prevax_extf-main-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-main-depression.rds

  cox_ipw-cohort_prevax_extf-main-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-main-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-main-depression.csv

  make_model_input-cohort_prevax_extf-main-eating_disorders:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-eating_disorders
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-main-eating_disorders.rds

  cox_ipw-cohort_prevax_extf-main-eating_disorders:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-eating_disorders.csv
    needs:
    - make_model_input-cohort_prevax_extf-main-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-main-eating_disorders.csv

  make_model_input-cohort_prevax_extf-main-self_harm:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-self_harm
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-main-self_harm.rds

  cox_ipw-cohort_prevax_extf-main-self_harm:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-self_harm.csv
    needs:
    - make_model_input-cohort_prevax_extf-main-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-main-self_harm.csv

  make_model_input-cohort_prevax_extf-main-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-main-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-main-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-main-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-main-serious_mental_illness.csv

  make_model_input-cohort_prevax_extf-main-suicide:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-main-suicide.rds

  cox_ipw-cohort_prevax_extf-main-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-suicide.csv
    needs:
    - make_model_input-cohort_prevax_extf-main-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-main-suicide.csv

  make_model_input-cohort_unvax_extf-main-addiction:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-addiction
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-main-addiction.rds

  cox_ipw-cohort_unvax_extf-main-addiction:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-main-addiction.csv
    needs:
    - make_model_input-cohort_unvax_extf-main-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-main-addiction.csv

  make_model_input-cohort_unvax_extf-main-anxiety_general:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-anxiety_general
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-main-anxiety_general.rds

  cox_ipw-cohort_unvax_extf-main-anxiety_general:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-main-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax_extf-main-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-main-anxiety_general.csv

  make_model_input-cohort_unvax_extf-main-anxiety_ptsd:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-anxiety_ptsd
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-main-anxiety_ptsd.rds

  cox_ipw-cohort_unvax_extf-main-anxiety_ptsd:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-main-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_unvax_extf-main-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-main-anxiety_ptsd.csv

  make_model_input-cohort_unvax_extf-main-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-main-depression.rds

  cox_ipw-cohort_unvax_extf-main-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-main-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-main-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-main-depression.csv

  make_model_input-cohort_unvax_extf-main-eating_disorders:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-eating_disorders
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-main-eating_disorders.rds

  cox_ipw-cohort_unvax_extf-main-eating_disorders:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-main-eating_disorders.csv
    needs:
    - make_model_input-cohort_unvax_extf-main-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-main-eating_disorders.csv

  make_model_input-cohort_unvax_extf-main-self_harm:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-self_harm
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-main-self_harm.rds

  cox_ipw-cohort_unvax_extf-main-self_harm:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-main-self_harm.csv
    needs:
    - make_model_input-cohort_unvax_extf-main-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-main-self_harm.csv

  make_model_input-cohort_unvax_extf-main-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-main-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-main-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-main-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-main-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-main-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-main-suicide:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-main-suicide.rds

  cox_ipw-cohort_unvax_extf-main-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-main-suicide.csv
    needs:
    - make_model_input-cohort_unvax_extf-main-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-main-suicide.csv

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

  cox_ipw-cohort_vax-main-addiction:
    run: cox-ipw:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-main-anxiety_general
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-anxiety_general.rds

  cox_ipw-cohort_vax-main-anxiety_general:
    run: cox-ipw:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_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_ptsd:
    run: r:latest analysis/make_model_input.R cohort_vax-main-anxiety_ptsd
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-anxiety_ptsd.rds

  cox_ipw-cohort_vax-main-anxiety_ptsd:
    run: cox-ipw:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-main-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-depression.rds

  cox_ipw-cohort_vax-main-depression:
    run: cox-ipw:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-main-eating_disorders
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-eating_disorders.rds

  cox_ipw-cohort_vax-main-eating_disorders:
    run: cox-ipw:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-main-self_harm
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-self_harm.rds

  cox_ipw-cohort_vax-main-self_harm:
    run: cox-ipw:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-main-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-main-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-suicide.rds

  cox_ipw-cohort_vax-main-suicide:
    run: cox-ipw:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_age_18_39-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_18_39-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_age_18_39-depression.rds

  cox_ipw-cohort_prevax_extf-sub_age_18_39-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_18_39-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_age_18_39-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_age_18_39-depression.csv

  make_model_input-cohort_prevax_extf-sub_age_18_39-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_18_39-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_age_18_39-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_age_18_39-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_18_39-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_age_18_39-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_age_18_39-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_age_18_39-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_18_39-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_age_18_39-depression.rds

  cox_ipw-cohort_unvax_extf-sub_age_18_39-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_age_18_39-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_age_18_39-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_age_18_39-depression.csv

  make_model_input-cohort_unvax_extf-sub_age_18_39-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_18_39-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_age_18_39-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_age_18_39-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_age_18_39-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_age_18_39-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_age_18_39-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_age_18_39-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_age_18_39-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_age_18_39-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_age_40_59-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_40_59-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_age_40_59-depression.rds

  cox_ipw-cohort_prevax_extf-sub_age_40_59-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_40_59-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_age_40_59-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_age_40_59-depression.csv

  make_model_input-cohort_prevax_extf-sub_age_40_59-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_40_59-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_age_40_59-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_age_40_59-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_40_59-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_age_40_59-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_age_40_59-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_age_40_59-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_40_59-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_age_40_59-depression.rds

  cox_ipw-cohort_unvax_extf-sub_age_40_59-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_age_40_59-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_age_40_59-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_age_40_59-depression.csv

  make_model_input-cohort_unvax_extf-sub_age_40_59-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_40_59-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_age_40_59-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_age_40_59-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_age_40_59-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_age_40_59-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_age_40_59-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_age_40_59-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_age_40_59-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_age_40_59-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_age_60_79-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_60_79-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_age_60_79-depression.rds

  cox_ipw-cohort_prevax_extf-sub_age_60_79-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_60_79-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_age_60_79-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_age_60_79-depression.csv

  make_model_input-cohort_prevax_extf-sub_age_60_79-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_60_79-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_age_60_79-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_age_60_79-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_60_79-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_age_60_79-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_age_60_79-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_age_60_79-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_60_79-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_age_60_79-depression.rds

  cox_ipw-cohort_unvax_extf-sub_age_60_79-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_age_60_79-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_age_60_79-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_age_60_79-depression.csv

  make_model_input-cohort_unvax_extf-sub_age_60_79-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_60_79-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_age_60_79-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_age_60_79-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_age_60_79-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_age_60_79-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_age_60_79-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_age_60_79-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_age_60_79-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_age_60_79-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_age_80_110-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_80_110-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_age_80_110-depression.rds

  cox_ipw-cohort_prevax_extf-sub_age_80_110-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_80_110-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_age_80_110-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_age_80_110-depression.csv

  make_model_input-cohort_prevax_extf-sub_age_80_110-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_80_110-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_age_80_110-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_age_80_110-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_80_110-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_age_80_110-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_age_80_110-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_age_80_110-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_80_110-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_age_80_110-depression.rds

  cox_ipw-cohort_unvax_extf-sub_age_80_110-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_age_80_110-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_age_80_110-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_age_80_110-depression.csv

  make_model_input-cohort_unvax_extf-sub_age_80_110-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_80_110-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_age_80_110-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_age_80_110-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_age_80_110-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_age_80_110-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_age_80_110-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_age_80_110-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_age_80_110-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_age_80_110-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_history-addiction:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_history-addiction
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_history-addiction.rds

  cox_ipw-cohort_unvax_extf-sub_covid_history-addiction:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_history-addiction.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_history-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_history-addiction.csv

  make_model_input-cohort_unvax_extf-sub_covid_history-anxiety_general:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_history-anxiety_general
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_history-anxiety_general.rds

  cox_ipw-cohort_unvax_extf-sub_covid_history-anxiety_general:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_history-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_history-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_history-anxiety_general.csv

  make_model_input-cohort_unvax_extf-sub_covid_history-anxiety_ptsd:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_history-anxiety_ptsd
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_history-anxiety_ptsd.rds

  cox_ipw-cohort_unvax_extf-sub_covid_history-anxiety_ptsd:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_history-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_history-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_history-anxiety_ptsd.csv

  make_model_input-cohort_unvax_extf-sub_covid_history-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_history-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_history-depression.rds

  cox_ipw-cohort_unvax_extf-sub_covid_history-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_history-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_history-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_history-depression.csv

  make_model_input-cohort_unvax_extf-sub_covid_history-eating_disorders:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_history-eating_disorders
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_history-eating_disorders.rds

  cox_ipw-cohort_unvax_extf-sub_covid_history-eating_disorders:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_history-eating_disorders.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_history-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_history-eating_disorders.csv

  make_model_input-cohort_unvax_extf-sub_covid_history-self_harm:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_history-self_harm
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_history-self_harm.rds

  cox_ipw-cohort_unvax_extf-sub_covid_history-self_harm:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_history-self_harm.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_history-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_history-self_harm.csv

  make_model_input-cohort_unvax_extf-sub_covid_history-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_history-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_history-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_covid_history-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_history-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_history-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_history-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_covid_history-suicide:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_history-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_history-suicide.rds

  cox_ipw-cohort_unvax_extf-sub_covid_history-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_history-suicide.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_history-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_history-suicide.csv

  make_model_input-cohort_vax-sub_covid_history-addiction:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_history-addiction
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_history-anxiety_general
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_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_ptsd:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_history-anxiety_ptsd
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_history-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_history-eating_disorders
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_history-self_harm
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_history-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_history-suicide
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_hospitalised-addiction:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-addiction
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-addiction.rds

  cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-addiction:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-addiction.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-addiction.csv

  make_model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-anxiety_general
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general.rds

  cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general.csv

  make_model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd.rds

  cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd.csv

  make_model_input-cohort_prevax_extf-sub_covid_hospitalised-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-depression.rds

  cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-depression.csv

  make_model_input-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-eating_disorders
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders.rds

  cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders.csv

  make_model_input-cohort_prevax_extf-sub_covid_hospitalised-self_harm:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-self_harm
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-self_harm.rds

  cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-self_harm:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-self_harm.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-self_harm.csv

  make_model_input-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness.csv

  make_model_input-cohort_prevax_extf-sub_covid_hospitalised-suicide:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_hospitalised-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_hospitalised-suicide.rds

  cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_hospitalised-suicide.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_hospitalised-suicide.csv

  make_model_input-cohort_unvax_extf-sub_covid_hospitalised-addiction:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_hospitalised-addiction
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_hospitalised-addiction.rds

  cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-addiction:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_hospitalised-addiction.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_hospitalised-addiction.csv

  make_model_input-cohort_unvax_extf-sub_covid_hospitalised-anxiety_general:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_hospitalised-anxiety_general
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_hospitalised-anxiety_general.rds

  cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-anxiety_general:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_hospitalised-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_hospitalised-anxiety_general.csv

  make_model_input-cohort_unvax_extf-sub_covid_hospitalised-anxiety_ptsd:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_hospitalised-anxiety_ptsd
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_hospitalised-anxiety_ptsd.rds

  cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-anxiety_ptsd:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_hospitalised-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_hospitalised-anxiety_ptsd.csv

  make_model_input-cohort_unvax_extf-sub_covid_hospitalised-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_hospitalised-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_hospitalised-depression.rds

  cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_hospitalised-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_hospitalised-depression.csv

  make_model_input-cohort_unvax_extf-sub_covid_hospitalised-eating_disorders:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_hospitalised-eating_disorders
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_hospitalised-eating_disorders.rds

  cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-eating_disorders:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_hospitalised-eating_disorders.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_hospitalised-eating_disorders.csv

  make_model_input-cohort_unvax_extf-sub_covid_hospitalised-self_harm:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_hospitalised-self_harm
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_hospitalised-self_harm.rds

  cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-self_harm:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_hospitalised-self_harm.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_hospitalised-self_harm.csv

  make_model_input-cohort_unvax_extf-sub_covid_hospitalised-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_hospitalised-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_hospitalised-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_hospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_hospitalised-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_covid_hospitalised-suicide:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_hospitalised-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_hospitalised-suicide.rds

  cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_hospitalised-suicide.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_hospitalised-suicide.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-addiction:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_hospitalised-addiction
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_hospitalised-anxiety_general
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_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_ptsd:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_hospitalised-anxiety_ptsd
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_hospitalised-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_hospitalised-eating_disorders
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_hospitalised-self_harm
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_hospitalised-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_hospitalised-suicide
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_nonhospitalised-addiction:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-addiction
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-addiction.rds

  cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-addiction:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-addiction.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-addiction.csv

  make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general.rds

  cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general.csv

  make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd.rds

  cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd.csv

  make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-depression.rds

  cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-depression.csv

  make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders.rds

  cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders.csv

  make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-self_harm
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm.rds

  cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm.csv

  make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness.csv

  make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-suicide:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_covid_nonhospitalised-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_covid_nonhospitalised-suicide.rds

  cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_covid_nonhospitalised-suicide.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_covid_nonhospitalised-suicide.csv

  make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-addiction:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_nonhospitalised-addiction
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_nonhospitalised-addiction.rds

  cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-addiction:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_nonhospitalised-addiction.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-addiction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_nonhospitalised-addiction.csv

  make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_general:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_general
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_general.rds

  cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_general:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_nonhospitalised-anxiety_general.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_general
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_general.csv

  make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_ptsd:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_ptsd
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_ptsd.rds

  cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_ptsd:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_nonhospitalised-anxiety_ptsd.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_ptsd
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_ptsd.csv

  make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_nonhospitalised-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_nonhospitalised-depression.rds

  cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_nonhospitalised-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_nonhospitalised-depression.csv

  make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-eating_disorders:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_nonhospitalised-eating_disorders
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_nonhospitalised-eating_disorders.rds

  cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-eating_disorders:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_nonhospitalised-eating_disorders.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-eating_disorders
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_nonhospitalised-eating_disorders.csv

  make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-self_harm:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_nonhospitalised-self_harm
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_nonhospitalised-self_harm.rds

  cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-self_harm:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_nonhospitalised-self_harm.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-self_harm
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_nonhospitalised-self_harm.csv

  make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_nonhospitalised-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_nonhospitalised-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_nonhospitalised-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_nonhospitalised-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-suicide:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_covid_nonhospitalised-suicide
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_covid_nonhospitalised-suicide.rds

  cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-suicide:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_covid_nonhospitalised-suicide.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-suicide
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_covid_nonhospitalised-suicide.csv

  make_model_input-cohort_vax-sub_covid_nonhospitalised-addiction:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_nonhospitalised-addiction
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_nonhospitalised-anxiety_general
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_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_ptsd:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_nonhospitalised-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_nonhospitalised-eating_disorders
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_nonhospitalised-self_harm
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_nonhospitalised-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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/make_model_input.R cohort_vax-sub_covid_nonhospitalised-suicide
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_asian-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_asian-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_asian-depression.rds

  cox_ipw-cohort_prevax_extf-sub_ethnicity_asian-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_asian-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_ethnicity_asian-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_asian-depression.csv

  make_model_input-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_ethnicity_asian-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_ethnicity_asian-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_ethnicity_asian-depression.rds

  cox_ipw-cohort_unvax_extf-sub_ethnicity_asian-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_asian-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_ethnicity_asian-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_ethnicity_asian-depression.csv

  make_model_input-cohort_unvax_extf-sub_ethnicity_asian-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_ethnicity_asian-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_ethnicity_asian-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_ethnicity_asian-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_asian-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_ethnicity_asian-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_ethnicity_asian-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_ethnicity_asian-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_asian-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_asian-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_black-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_black-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_black-depression.rds

  cox_ipw-cohort_prevax_extf-sub_ethnicity_black-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_black-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_ethnicity_black-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_black-depression.csv

  make_model_input-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_ethnicity_black-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_ethnicity_black-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_ethnicity_black-depression.rds

  cox_ipw-cohort_unvax_extf-sub_ethnicity_black-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_black-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_ethnicity_black-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_ethnicity_black-depression.csv

  make_model_input-cohort_unvax_extf-sub_ethnicity_black-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_ethnicity_black-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_ethnicity_black-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_ethnicity_black-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_black-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_ethnicity_black-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_ethnicity_black-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_ethnicity_black-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_black-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_black-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_mixed-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_mixed-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_mixed-depression.rds

  cox_ipw-cohort_prevax_extf-sub_ethnicity_mixed-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_mixed-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_ethnicity_mixed-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_mixed-depression.csv

  make_model_input-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_ethnicity_mixed-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_ethnicity_mixed-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_ethnicity_mixed-depression.rds

  cox_ipw-cohort_unvax_extf-sub_ethnicity_mixed-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_mixed-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_ethnicity_mixed-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_ethnicity_mixed-depression.csv

  make_model_input-cohort_unvax_extf-sub_ethnicity_mixed-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_ethnicity_mixed-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_ethnicity_mixed-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_ethnicity_mixed-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_mixed-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_ethnicity_mixed-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_ethnicity_mixed-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_ethnicity_mixed-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_mixed-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_mixed-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_other-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_other-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_other-depression.rds

  cox_ipw-cohort_prevax_extf-sub_ethnicity_other-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_other-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_ethnicity_other-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_other-depression.csv

  make_model_input-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_ethnicity_other-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_ethnicity_other-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_ethnicity_other-depression.rds

  cox_ipw-cohort_unvax_extf-sub_ethnicity_other-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_other-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_ethnicity_other-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_ethnicity_other-depression.csv

  make_model_input-cohort_unvax_extf-sub_ethnicity_other-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_ethnicity_other-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_ethnicity_other-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_ethnicity_other-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_other-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_ethnicity_other-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_ethnicity_other-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_ethnicity_other-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_other-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_other-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_white-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_white-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_white-depression.rds

  cox_ipw-cohort_prevax_extf-sub_ethnicity_white-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_white-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_ethnicity_white-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_white-depression.csv

  make_model_input-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_ethnicity_white-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_ethnicity_white-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_ethnicity_white-depression.rds

  cox_ipw-cohort_unvax_extf-sub_ethnicity_white-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_white-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_ethnicity_white-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_ethnicity_white-depression.csv

  make_model_input-cohort_unvax_extf-sub_ethnicity_white-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_ethnicity_white-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_ethnicity_white-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_ethnicity_white-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_ethnicity_white-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_ethnicity_white-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_ethnicity_white-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_ethnicity_white-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_white-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_white-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_history_none-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_none-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_history_none-depression.rds

  cox_ipw-cohort_prevax_extf-sub_history_none-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_none-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_history_none-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_history_none-depression.csv

  make_model_input-cohort_prevax_extf-sub_history_none-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_none-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_history_none-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_history_none-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_none-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_history_none-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_history_none-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_history_none-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_history_none-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_history_none-depression.rds

  cox_ipw-cohort_unvax_extf-sub_history_none-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_history_none-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_history_none-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_history_none-depression.csv

  make_model_input-cohort_unvax_extf-sub_history_none-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_history_none-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_history_none-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_history_none-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_history_none-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_history_none-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_history_none-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_history_none-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_history_none-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_history_none-depression.rds

  cox_ipw-cohort_vax-sub_history_none-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_history_none-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_history_none-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_history_none-depression.csv

  make_model_input-cohort_vax-sub_history_none-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_history_none-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_history_none-serious_mental_illness.rds

  cox_ipw-cohort_vax-sub_history_none-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_history_none-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_history_none-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_history_none-serious_mental_illness.csv

  make_model_input-cohort_prevax_extf-sub_history_notrecent-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_notrecent-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_history_notrecent-depression.rds

  cox_ipw-cohort_prevax_extf-sub_history_notrecent-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_notrecent-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_history_notrecent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_history_notrecent-depression.csv

  make_model_input-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_notrecent-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_history_notrecent-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_history_notrecent-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_history_notrecent-depression.rds

  cox_ipw-cohort_unvax_extf-sub_history_notrecent-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_history_notrecent-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_history_notrecent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_history_notrecent-depression.csv

  make_model_input-cohort_unvax_extf-sub_history_notrecent-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_history_notrecent-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_history_notrecent-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_history_notrecent-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_history_notrecent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_history_notrecent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_history_notrecent-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_history_notrecent-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_history_notrecent-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_history_notrecent-depression.rds

  cox_ipw-cohort_vax-sub_history_notrecent-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_history_notrecent-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_history_notrecent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_history_notrecent-depression.csv

  make_model_input-cohort_vax-sub_history_notrecent-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_history_notrecent-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_history_notrecent-serious_mental_illness.rds

  cox_ipw-cohort_vax-sub_history_notrecent-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_history_notrecent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_history_notrecent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_history_notrecent-serious_mental_illness.csv

  make_model_input-cohort_prevax_extf-sub_history_recent-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_recent-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_history_recent-depression.rds

  cox_ipw-cohort_prevax_extf-sub_history_recent-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_recent-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_history_recent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_history_recent-depression.csv

  make_model_input-cohort_prevax_extf-sub_history_recent-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_history_recent-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_history_recent-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_history_recent-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_history_recent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_history_recent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_history_recent-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_history_recent-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_history_recent-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_history_recent-depression.rds

  cox_ipw-cohort_unvax_extf-sub_history_recent-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_history_recent-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_history_recent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_history_recent-depression.csv

  make_model_input-cohort_unvax_extf-sub_history_recent-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_history_recent-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_history_recent-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_history_recent-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_history_recent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_history_recent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_history_recent-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_history_recent-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_history_recent-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_history_recent-depression.rds

  cox_ipw-cohort_vax-sub_history_recent-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-sub_history_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_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_history_recent-depression.csv
    needs:
    - make_model_input-cohort_vax-sub_history_recent-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_history_recent-depression.csv

  make_model_input-cohort_vax-sub_history_recent-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_history_recent-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_history_recent-serious_mental_illness.rds

  cox_ipw-cohort_vax-sub_history_recent-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-sub_history_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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_history_recent-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_vax-sub_history_recent-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_history_recent-serious_mental_illness.csv

  make_model_input-cohort_prevax_extf-sub_sex_female-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_sex_female-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_sex_female-depression.rds

  cox_ipw-cohort_prevax_extf-sub_sex_female-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_sex_female-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_sex_female-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_sex_female-depression.csv

  make_model_input-cohort_prevax_extf-sub_sex_female-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_sex_female-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_sex_female-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_sex_female-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_sex_female-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_sex_female-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_sex_female-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_sex_female-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_sex_female-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_sex_female-depression.rds

  cox_ipw-cohort_unvax_extf-sub_sex_female-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_sex_female-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_sex_female-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_sex_female-depression.csv

  make_model_input-cohort_unvax_extf-sub_sex_female-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_sex_female-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_sex_female-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_sex_female-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_sex_female-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_sex_female-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_sex_female-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_sex_female-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_sex_female-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_sex_female-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_sex_male-depression:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_sex_male-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_sex_male-depression.rds

  cox_ipw-cohort_prevax_extf-sub_sex_male-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_sex_male-depression.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_sex_male-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_sex_male-depression.csv

  make_model_input-cohort_prevax_extf-sub_sex_male-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_sex_male-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax_extf-sub_sex_male-serious_mental_illness.rds

  cox_ipw-cohort_prevax_extf-sub_sex_male-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=10 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-sub_sex_male-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_prevax_extf-sub_sex_male-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax_extf-sub_sex_male-serious_mental_illness.csv

  make_model_input-cohort_unvax_extf-sub_sex_male-depression:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_sex_male-depression
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_sex_male-depression.rds

  cox_ipw-cohort_unvax_extf-sub_sex_male-depression:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_sex_male-depression.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_sex_male-depression
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_sex_male-depression.csv

  make_model_input-cohort_unvax_extf-sub_sex_male-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_sex_male-serious_mental_illness
    needs:
    - replace_suicide
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax_extf-sub_sex_male-serious_mental_illness.rds

  cox_ipw-cohort_unvax_extf-sub_sex_male-serious_mental_illness:
    run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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_extf-sub_sex_male-serious_mental_illness.csv
    needs:
    - make_model_input-cohort_unvax_extf-sub_sex_male-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax_extf-sub_sex_male-serious_mental_illness.csv

  make_model_input-cohort_vax-sub_sex_male-depression:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_sex_male-depression
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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-serious_mental_illness:
    run: r:latest analysis/make_model_input.R cohort_vax-sub_sex_male-serious_mental_illness
    needs:
    - replace_suicide
    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:v0.0.25 --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_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
      --cox_start=index_date --cox_stop=end_date_outcome --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

  ## Table 2 - prevax_extf 

  table2_prevax_extf:
    run: r:latest analysis/table2.R prevax_extf
    needs:
    - make_model_input-cohort_prevax_extf-day0_main-depression
    - make_model_input-cohort_prevax_extf-day0_main-serious_mental_illness
    - make_model_input-cohort_prevax_extf-day0_main-suicide
    - make_model_input-cohort_prevax_extf-day0_sub_covid_hospitalised-depression
    - make_model_input-cohort_prevax_extf-day0_sub_covid_hospitalised-serious_mental_illness
    - make_model_input-cohort_prevax_extf-day0_sub_covid_hospitalised-suicide
    - make_model_input-cohort_prevax_extf-day0_sub_covid_nonhospitalised-depression
    - make_model_input-cohort_prevax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness
    - make_model_input-cohort_prevax_extf-day0_sub_covid_nonhospitalised-suicide
    - make_model_input-cohort_prevax_extf-day0_sub_history_none-depression
    - make_model_input-cohort_prevax_extf-day0_sub_history_none-serious_mental_illness
    - make_model_input-cohort_prevax_extf-day0_sub_history_notrecent-depression
    - make_model_input-cohort_prevax_extf-day0_sub_history_notrecent-serious_mental_illness
    - make_model_input-cohort_prevax_extf-day0_sub_history_recent-depression
    - make_model_input-cohort_prevax_extf-day0_sub_history_recent-serious_mental_illness
    - make_model_input-cohort_prevax_extf-main-addiction
    - make_model_input-cohort_prevax_extf-main-anxiety_general
    - make_model_input-cohort_prevax_extf-main-anxiety_ptsd
    - make_model_input-cohort_prevax_extf-main-depression
    - make_model_input-cohort_prevax_extf-main-eating_disorders
    - make_model_input-cohort_prevax_extf-main-self_harm
    - make_model_input-cohort_prevax_extf-main-serious_mental_illness
    - make_model_input-cohort_prevax_extf-main-suicide
    - make_model_input-cohort_prevax_extf-sub_age_18_39-depression
    - make_model_input-cohort_prevax_extf-sub_age_18_39-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_age_40_59-depression
    - make_model_input-cohort_prevax_extf-sub_age_40_59-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_age_60_79-depression
    - make_model_input-cohort_prevax_extf-sub_age_60_79-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_age_80_110-depression
    - make_model_input-cohort_prevax_extf-sub_age_80_110-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-addiction
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-depression
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-self_harm
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_covid_hospitalised-suicide
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-addiction
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-depression
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_covid_nonhospitalised-suicide
    - make_model_input-cohort_prevax_extf-sub_ethnicity_asian-depression
    - make_model_input-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_ethnicity_black-depression
    - make_model_input-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_ethnicity_mixed-depression
    - make_model_input-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_ethnicity_other-depression
    - make_model_input-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_ethnicity_white-depression
    - make_model_input-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_history_none-depression
    - make_model_input-cohort_prevax_extf-sub_history_none-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_history_notrecent-depression
    - make_model_input-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_history_recent-depression
    - make_model_input-cohort_prevax_extf-sub_history_recent-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_sex_female-depression
    - make_model_input-cohort_prevax_extf-sub_sex_female-serious_mental_illness
    - make_model_input-cohort_prevax_extf-sub_sex_male-depression
    - make_model_input-cohort_prevax_extf-sub_sex_male-serious_mental_illness
    outputs:
      moderately_sensitive:
        table2: output/table2_prevax_extf.csv
        table2_rounded: output/table2_prevax_extf_rounded.csv

  ## Table 2 - unvax_extf 

  table2_unvax_extf:
    run: r:latest analysis/table2.R unvax_extf
    needs:
    - make_model_input-cohort_unvax_extf-day0_main-depression
    - make_model_input-cohort_unvax_extf-day0_main-serious_mental_illness
    - make_model_input-cohort_unvax_extf-day0_main-suicide
    - make_model_input-cohort_unvax_extf-day0_sub_covid_hospitalised-depression
    - make_model_input-cohort_unvax_extf-day0_sub_covid_hospitalised-serious_mental_illness
    - make_model_input-cohort_unvax_extf-day0_sub_covid_hospitalised-suicide
    - make_model_input-cohort_unvax_extf-day0_sub_covid_nonhospitalised-depression
    - make_model_input-cohort_unvax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness
    - make_model_input-cohort_unvax_extf-day0_sub_covid_nonhospitalised-suicide
    - make_model_input-cohort_unvax_extf-day0_sub_history_none-depression
    - make_model_input-cohort_unvax_extf-day0_sub_history_none-serious_mental_illness
    - make_model_input-cohort_unvax_extf-day0_sub_history_notrecent-depression
    - make_model_input-cohort_unvax_extf-day0_sub_history_notrecent-serious_mental_illness
    - make_model_input-cohort_unvax_extf-day0_sub_history_recent-depression
    - make_model_input-cohort_unvax_extf-day0_sub_history_recent-serious_mental_illness
    - make_model_input-cohort_unvax_extf-main-addiction
    - make_model_input-cohort_unvax_extf-main-anxiety_general
    - make_model_input-cohort_unvax_extf-main-anxiety_ptsd
    - make_model_input-cohort_unvax_extf-main-depression
    - make_model_input-cohort_unvax_extf-main-eating_disorders
    - make_model_input-cohort_unvax_extf-main-self_harm
    - make_model_input-cohort_unvax_extf-main-serious_mental_illness
    - make_model_input-cohort_unvax_extf-main-suicide
    - make_model_input-cohort_unvax_extf-sub_age_18_39-depression
    - make_model_input-cohort_unvax_extf-sub_age_18_39-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_age_40_59-depression
    - make_model_input-cohort_unvax_extf-sub_age_40_59-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_age_60_79-depression
    - make_model_input-cohort_unvax_extf-sub_age_60_79-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_age_80_110-depression
    - make_model_input-cohort_unvax_extf-sub_age_80_110-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_covid_history-addiction
    - make_model_input-cohort_unvax_extf-sub_covid_history-anxiety_general
    - make_model_input-cohort_unvax_extf-sub_covid_history-anxiety_ptsd
    - make_model_input-cohort_unvax_extf-sub_covid_history-depression
    - make_model_input-cohort_unvax_extf-sub_covid_history-eating_disorders
    - make_model_input-cohort_unvax_extf-sub_covid_history-self_harm
    - make_model_input-cohort_unvax_extf-sub_covid_history-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_covid_history-suicide
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-addiction
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-anxiety_general
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-anxiety_ptsd
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-depression
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-eating_disorders
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-self_harm
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_covid_hospitalised-suicide
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-addiction
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_general
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_ptsd
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-depression
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-eating_disorders
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-self_harm
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_covid_nonhospitalised-suicide
    - make_model_input-cohort_unvax_extf-sub_ethnicity_asian-depression
    - make_model_input-cohort_unvax_extf-sub_ethnicity_asian-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_ethnicity_black-depression
    - make_model_input-cohort_unvax_extf-sub_ethnicity_black-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_ethnicity_mixed-depression
    - make_model_input-cohort_unvax_extf-sub_ethnicity_mixed-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_ethnicity_other-depression
    - make_model_input-cohort_unvax_extf-sub_ethnicity_other-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_ethnicity_white-depression
    - make_model_input-cohort_unvax_extf-sub_ethnicity_white-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_history_none-depression
    - make_model_input-cohort_unvax_extf-sub_history_none-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_history_notrecent-depression
    - make_model_input-cohort_unvax_extf-sub_history_notrecent-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_history_recent-depression
    - make_model_input-cohort_unvax_extf-sub_history_recent-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_sex_female-depression
    - make_model_input-cohort_unvax_extf-sub_sex_female-serious_mental_illness
    - make_model_input-cohort_unvax_extf-sub_sex_male-depression
    - make_model_input-cohort_unvax_extf-sub_sex_male-serious_mental_illness
    outputs:
      moderately_sensitive:
        table2: output/table2_unvax_extf.csv
        table2_rounded: output/table2_unvax_extf_rounded.csv

  ## Table 2 - vax 

  table2_vax:
    run: r:latest analysis/table2.R vax
    needs:
    - make_model_input-cohort_vax-day0_main-depression
    - make_model_input-cohort_vax-day0_main-serious_mental_illness
    - make_model_input-cohort_vax-day0_main-suicide
    - make_model_input-cohort_vax-day0_sub_covid_hospitalised-depression
    - make_model_input-cohort_vax-day0_sub_covid_hospitalised-serious_mental_illness
    - make_model_input-cohort_vax-day0_sub_covid_hospitalised-suicide
    - make_model_input-cohort_vax-day0_sub_covid_nonhospitalised-depression
    - make_model_input-cohort_vax-day0_sub_covid_nonhospitalised-serious_mental_illness
    - make_model_input-cohort_vax-day0_sub_covid_nonhospitalised-suicide
    - make_model_input-cohort_vax-day0_sub_history_none-depression
    - make_model_input-cohort_vax-day0_sub_history_none-serious_mental_illness
    - make_model_input-cohort_vax-day0_sub_history_notrecent-depression
    - make_model_input-cohort_vax-day0_sub_history_notrecent-serious_mental_illness
    - make_model_input-cohort_vax-day0_sub_history_recent-depression
    - make_model_input-cohort_vax-day0_sub_history_recent-serious_mental_illness
    - make_model_input-cohort_vax-main-addiction
    - make_model_input-cohort_vax-main-anxiety_general
    - make_model_input-cohort_vax-main-anxiety_ptsd
    - make_model_input-cohort_vax-main-depression
    - make_model_input-cohort_vax-main-eating_disorders
    - make_model_input-cohort_vax-main-self_harm
    - make_model_input-cohort_vax-main-serious_mental_illness
    - make_model_input-cohort_vax-main-suicide
    - make_model_input-cohort_vax-sub_age_18_39-depression
    - make_model_input-cohort_vax-sub_age_18_39-serious_mental_illness
    - make_model_input-cohort_vax-sub_age_40_59-depression
    - make_model_input-cohort_vax-sub_age_40_59-serious_mental_illness
    - make_model_input-cohort_vax-sub_age_60_79-depression
    - make_model_input-cohort_vax-sub_age_60_79-serious_mental_illness
    - make_model_input-cohort_vax-sub_age_80_110-depression
    - make_model_input-cohort_vax-sub_age_80_110-serious_mental_illness
    - make_model_input-cohort_vax-sub_covid_history-addiction
    - make_model_input-cohort_vax-sub_covid_history-anxiety_general
    - make_model_input-cohort_vax-sub_covid_history-anxiety_ptsd
    - make_model_input-cohort_vax-sub_covid_history-depression
    - make_model_input-cohort_vax-sub_covid_history-eating_disorders
    - make_model_input-cohort_vax-sub_covid_history-self_harm
    - make_model_input-cohort_vax-sub_covid_history-serious_mental_illness
    - make_model_input-cohort_vax-sub_covid_history-suicide
    - make_model_input-cohort_vax-sub_covid_hospitalised-addiction
    - make_model_input-cohort_vax-sub_covid_hospitalised-anxiety_general
    - make_model_input-cohort_vax-sub_covid_hospitalised-anxiety_ptsd
    - make_model_input-cohort_vax-sub_covid_hospitalised-depression
    - make_model_input-cohort_vax-sub_covid_hospitalised-eating_disorders
    - make_model_input-cohort_vax-sub_covid_hospitalised-self_harm
    - make_model_input-cohort_vax-sub_covid_hospitalised-serious_mental_illness
    - make_model_input-cohort_vax-sub_covid_hospitalised-suicide
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-addiction
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-anxiety_general
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-depression
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-eating_disorders
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-self_harm
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-suicide
    - make_model_input-cohort_vax-sub_ethnicity_asian-depression
    - make_model_input-cohort_vax-sub_ethnicity_asian-serious_mental_illness
    - make_model_input-cohort_vax-sub_ethnicity_black-depression
    - make_model_input-cohort_vax-sub_ethnicity_black-serious_mental_illness
    - make_model_input-cohort_vax-sub_ethnicity_mixed-depression
    - make_model_input-cohort_vax-sub_ethnicity_mixed-serious_mental_illness
    - make_model_input-cohort_vax-sub_ethnicity_other-depression
    - make_model_input-cohort_vax-sub_ethnicity_other-serious_mental_illness
    - make_model_input-cohort_vax-sub_ethnicity_white-depression
    - make_model_input-cohort_vax-sub_ethnicity_white-serious_mental_illness
    - make_model_input-cohort_vax-sub_history_none-depression
    - make_model_input-cohort_vax-sub_history_none-serious_mental_illness
    - make_model_input-cohort_vax-sub_history_notrecent-depression
    - make_model_input-cohort_vax-sub_history_notrecent-serious_mental_illness
    - make_model_input-cohort_vax-sub_history_recent-depression
    - make_model_input-cohort_vax-sub_history_recent-serious_mental_illness
    - make_model_input-cohort_vax-sub_sex_female-depression
    - make_model_input-cohort_vax-sub_sex_female-serious_mental_illness
    - make_model_input-cohort_vax-sub_sex_male-depression
    - make_model_input-cohort_vax-sub_sex_male-serious_mental_illness
    outputs:
      moderately_sensitive:
        table2: output/table2_vax.csv
        table2_rounded: output/table2_vax_rounded.csv

  ## Venn - prevax_extf 

  venn_prevax_extf:
    run: r:latest analysis/venn.R prevax_extf
    needs:
    - preprocess_data_prevax_extf
    - make_model_input-cohort_prevax_extf-main-depression
    - make_model_input-cohort_prevax_extf-main-serious_mental_illness
    - make_model_input-cohort_prevax_extf-main-suicide
    - make_model_input-cohort_prevax_extf-main-addiction
    - make_model_input-cohort_prevax_extf-main-anxiety_general
    - make_model_input-cohort_prevax_extf-main-anxiety_ptsd
    - make_model_input-cohort_prevax_extf-main-eating_disorders
    - make_model_input-cohort_prevax_extf-main-self_harm
    outputs:
      moderately_sensitive:
        venn: output/venn_prevax_extf.csv
        venn_rounded: output/venn_prevax_extf_rounded.csv

  ## Venn - unvax_extf 

  venn_unvax_extf:
    run: r:latest analysis/venn.R unvax_extf
    needs:
    - preprocess_data_unvax_extf
    - make_model_input-cohort_unvax_extf-main-depression
    - make_model_input-cohort_unvax_extf-main-serious_mental_illness
    - make_model_input-cohort_unvax_extf-main-suicide
    - make_model_input-cohort_unvax_extf-main-addiction
    - make_model_input-cohort_unvax_extf-main-anxiety_general
    - make_model_input-cohort_unvax_extf-main-anxiety_ptsd
    - make_model_input-cohort_unvax_extf-main-eating_disorders
    - make_model_input-cohort_unvax_extf-main-self_harm
    outputs:
      moderately_sensitive:
        venn: output/venn_unvax_extf.csv
        venn_rounded: output/venn_unvax_extf_rounded.csv

  ## Venn - vax 

  venn_vax:
    run: r:latest analysis/venn.R vax
    needs:
    - preprocess_data_vax
    - make_model_input-cohort_vax-main-depression
    - make_model_input-cohort_vax-main-serious_mental_illness
    - make_model_input-cohort_vax-main-suicide
    - make_model_input-cohort_vax-main-addiction
    - make_model_input-cohort_vax-main-anxiety_general
    - make_model_input-cohort_vax-main-anxiety_ptsd
    - make_model_input-cohort_vax-main-eating_disorders
    - make_model_input-cohort_vax-main-self_harm
    outputs:
      moderately_sensitive:
        venn: output/venn_vax.csv
        venn_rounded: output/venn_vax_rounded.csv

  ## Stage 6 - make output 

  make_model_output:
    run: r:latest analysis/make_model_output.R
    needs:
    - cox_ipw-cohort_prevax_extf-day0_main-depression
    - cox_ipw-cohort_prevax_extf-day0_main-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-day0_main-suicide
    - cox_ipw-cohort_unvax_extf-day0_main-depression
    - cox_ipw-cohort_unvax_extf-day0_main-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-day0_main-suicide
    - cox_ipw-cohort_vax-day0_main-depression
    - cox_ipw-cohort_vax-day0_main-serious_mental_illness
    - cox_ipw-cohort_vax-day0_main-suicide
    - cox_ipw-cohort_prevax_extf-day0_sub_covid_hospitalised-depression
    - cox_ipw-cohort_prevax_extf-day0_sub_covid_hospitalised-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-day0_sub_covid_hospitalised-suicide
    - cox_ipw-cohort_unvax_extf-day0_sub_covid_hospitalised-depression
    - cox_ipw-cohort_unvax_extf-day0_sub_covid_hospitalised-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-day0_sub_covid_hospitalised-suicide
    - cox_ipw-cohort_vax-day0_sub_covid_hospitalised-depression
    - cox_ipw-cohort_vax-day0_sub_covid_hospitalised-serious_mental_illness
    - cox_ipw-cohort_vax-day0_sub_covid_hospitalised-suicide
    - cox_ipw-cohort_prevax_extf-day0_sub_covid_nonhospitalised-depression
    - cox_ipw-cohort_prevax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-day0_sub_covid_nonhospitalised-suicide
    - cox_ipw-cohort_unvax_extf-day0_sub_covid_nonhospitalised-depression
    - cox_ipw-cohort_unvax_extf-day0_sub_covid_nonhospitalised-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-day0_sub_covid_nonhospitalised-suicide
    - cox_ipw-cohort_vax-day0_sub_covid_nonhospitalised-depression
    - cox_ipw-cohort_vax-day0_sub_covid_nonhospitalised-serious_mental_illness
    - cox_ipw-cohort_vax-day0_sub_covid_nonhospitalised-suicide
    - cox_ipw-cohort_prevax_extf-day0_sub_history_none-depression
    - cox_ipw-cohort_prevax_extf-day0_sub_history_none-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-day0_sub_history_none-depression
    - cox_ipw-cohort_unvax_extf-day0_sub_history_none-serious_mental_illness
    - cox_ipw-cohort_vax-day0_sub_history_none-depression
    - cox_ipw-cohort_vax-day0_sub_history_none-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-day0_sub_history_notrecent-depression
    - cox_ipw-cohort_prevax_extf-day0_sub_history_notrecent-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-day0_sub_history_notrecent-depression
    - cox_ipw-cohort_unvax_extf-day0_sub_history_notrecent-serious_mental_illness
    - cox_ipw-cohort_vax-day0_sub_history_notrecent-depression
    - cox_ipw-cohort_vax-day0_sub_history_notrecent-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-day0_sub_history_recent-depression
    - cox_ipw-cohort_prevax_extf-day0_sub_history_recent-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-day0_sub_history_recent-depression
    - cox_ipw-cohort_unvax_extf-day0_sub_history_recent-serious_mental_illness
    - cox_ipw-cohort_vax-day0_sub_history_recent-depression
    - cox_ipw-cohort_vax-day0_sub_history_recent-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-main-addiction
    - cox_ipw-cohort_prevax_extf-main-anxiety_general
    - cox_ipw-cohort_prevax_extf-main-anxiety_ptsd
    - cox_ipw-cohort_prevax_extf-main-depression
    - cox_ipw-cohort_prevax_extf-main-eating_disorders
    - cox_ipw-cohort_prevax_extf-main-self_harm
    - cox_ipw-cohort_prevax_extf-main-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-main-suicide
    - cox_ipw-cohort_unvax_extf-main-addiction
    - cox_ipw-cohort_unvax_extf-main-anxiety_general
    - cox_ipw-cohort_unvax_extf-main-anxiety_ptsd
    - cox_ipw-cohort_unvax_extf-main-depression
    - cox_ipw-cohort_unvax_extf-main-eating_disorders
    - cox_ipw-cohort_unvax_extf-main-self_harm
    - cox_ipw-cohort_unvax_extf-main-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-main-suicide
    - cox_ipw-cohort_vax-main-addiction
    - cox_ipw-cohort_vax-main-anxiety_general
    - cox_ipw-cohort_vax-main-anxiety_ptsd
    - cox_ipw-cohort_vax-main-depression
    - cox_ipw-cohort_vax-main-self_harm
    - cox_ipw-cohort_vax-main-serious_mental_illness
    - cox_ipw-cohort_vax-main-suicide
    - cox_ipw-cohort_prevax_extf-sub_age_18_39-depression
    - cox_ipw-cohort_prevax_extf-sub_age_18_39-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_age_18_39-depression
    - cox_ipw-cohort_unvax_extf-sub_age_18_39-serious_mental_illness
    - cox_ipw-cohort_vax-sub_age_18_39-depression
    - cox_ipw-cohort_vax-sub_age_18_39-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_age_40_59-depression
    - cox_ipw-cohort_prevax_extf-sub_age_40_59-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_age_40_59-depression
    - cox_ipw-cohort_unvax_extf-sub_age_40_59-serious_mental_illness
    - cox_ipw-cohort_vax-sub_age_40_59-depression
    - cox_ipw-cohort_vax-sub_age_40_59-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_age_60_79-depression
    - cox_ipw-cohort_prevax_extf-sub_age_60_79-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_age_60_79-depression
    - cox_ipw-cohort_unvax_extf-sub_age_60_79-serious_mental_illness
    - cox_ipw-cohort_vax-sub_age_60_79-depression
    - cox_ipw-cohort_vax-sub_age_60_79-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_age_80_110-depression
    - cox_ipw-cohort_prevax_extf-sub_age_80_110-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_age_80_110-depression
    - cox_ipw-cohort_unvax_extf-sub_age_80_110-serious_mental_illness
    - cox_ipw-cohort_vax-sub_age_80_110-depression
    - cox_ipw-cohort_vax-sub_age_80_110-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_covid_history-addiction
    - cox_ipw-cohort_unvax_extf-sub_covid_history-anxiety_general
    - cox_ipw-cohort_unvax_extf-sub_covid_history-anxiety_ptsd
    - cox_ipw-cohort_unvax_extf-sub_covid_history-depression
    - cox_ipw-cohort_unvax_extf-sub_covid_history-eating_disorders
    - cox_ipw-cohort_unvax_extf-sub_covid_history-self_harm
    - cox_ipw-cohort_unvax_extf-sub_covid_history-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_covid_history-suicide
    - cox_ipw-cohort_vax-sub_covid_history-addiction
    - cox_ipw-cohort_vax-sub_covid_history-anxiety_general
    - cox_ipw-cohort_vax-sub_covid_history-anxiety_ptsd
    - cox_ipw-cohort_vax-sub_covid_history-depression
    - cox_ipw-cohort_vax-sub_covid_history-eating_disorders
    - cox_ipw-cohort_vax-sub_covid_history-self_harm
    - cox_ipw-cohort_vax-sub_covid_history-serious_mental_illness
    - cox_ipw-cohort_vax-sub_covid_history-suicide
    - cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-addiction
    - cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-anxiety_general
    - cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-anxiety_ptsd
    - cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-depression
    - cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-eating_disorders
    - cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-self_harm
    - cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_covid_hospitalised-suicide
    - cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-addiction
    - cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-anxiety_general
    - cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-anxiety_ptsd
    - cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-depression
    - cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-eating_disorders
    - cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-self_harm
    - cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_covid_hospitalised-suicide
    - cox_ipw-cohort_vax-sub_covid_hospitalised-addiction
    - cox_ipw-cohort_vax-sub_covid_hospitalised-anxiety_general
    - cox_ipw-cohort_vax-sub_covid_hospitalised-anxiety_ptsd
    - cox_ipw-cohort_vax-sub_covid_hospitalised-depression
    - cox_ipw-cohort_vax-sub_covid_hospitalised-eating_disorders
    - cox_ipw-cohort_vax-sub_covid_hospitalised-self_harm
    - cox_ipw-cohort_vax-sub_covid_hospitalised-serious_mental_illness
    - cox_ipw-cohort_vax-sub_covid_hospitalised-suicide
    - cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-addiction
    - cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_general
    - cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-anxiety_ptsd
    - cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-depression
    - cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-eating_disorders
    - cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-self_harm
    - cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_covid_nonhospitalised-suicide
    - cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-addiction
    - cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_general
    - cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-anxiety_ptsd
    - cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-depression
    - cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-eating_disorders
    - cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-self_harm
    - cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_covid_nonhospitalised-suicide
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-addiction
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-anxiety_general
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-anxiety_ptsd
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-depression
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-self_harm
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-serious_mental_illness
    - cox_ipw-cohort_vax-sub_covid_nonhospitalised-suicide
    - cox_ipw-cohort_prevax_extf-sub_ethnicity_asian-depression
    - cox_ipw-cohort_prevax_extf-sub_ethnicity_asian-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_ethnicity_asian-depression
    - cox_ipw-cohort_unvax_extf-sub_ethnicity_asian-serious_mental_illness
    - cox_ipw-cohort_vax-sub_ethnicity_asian-depression
    - cox_ipw-cohort_vax-sub_ethnicity_asian-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_ethnicity_black-depression
    - cox_ipw-cohort_prevax_extf-sub_ethnicity_black-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_ethnicity_black-depression
    - cox_ipw-cohort_unvax_extf-sub_ethnicity_black-serious_mental_illness
    - cox_ipw-cohort_vax-sub_ethnicity_black-depression
    - cox_ipw-cohort_vax-sub_ethnicity_black-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_ethnicity_mixed-depression
    - cox_ipw-cohort_prevax_extf-sub_ethnicity_mixed-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_ethnicity_mixed-depression
    - cox_ipw-cohort_unvax_extf-sub_ethnicity_mixed-serious_mental_illness
    - cox_ipw-cohort_vax-sub_ethnicity_mixed-depression
    - cox_ipw-cohort_vax-sub_ethnicity_mixed-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_ethnicity_other-depression
    - cox_ipw-cohort_prevax_extf-sub_ethnicity_other-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_ethnicity_other-depression
    - cox_ipw-cohort_unvax_extf-sub_ethnicity_other-serious_mental_illness
    - cox_ipw-cohort_vax-sub_ethnicity_other-depression
    - cox_ipw-cohort_vax-sub_ethnicity_other-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_ethnicity_white-depression
    - cox_ipw-cohort_prevax_extf-sub_ethnicity_white-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_ethnicity_white-depression
    - cox_ipw-cohort_unvax_extf-sub_ethnicity_white-serious_mental_illness
    - cox_ipw-cohort_vax-sub_ethnicity_white-depression
    - cox_ipw-cohort_vax-sub_ethnicity_white-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_history_none-depression
    - cox_ipw-cohort_prevax_extf-sub_history_none-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_history_none-depression
    - cox_ipw-cohort_unvax_extf-sub_history_none-serious_mental_illness
    - cox_ipw-cohort_vax-sub_history_none-depression
    - cox_ipw-cohort_vax-sub_history_none-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_history_notrecent-depression
    - cox_ipw-cohort_prevax_extf-sub_history_notrecent-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_history_notrecent-depression
    - cox_ipw-cohort_unvax_extf-sub_history_notrecent-serious_mental_illness
    - cox_ipw-cohort_vax-sub_history_notrecent-depression
    - cox_ipw-cohort_vax-sub_history_notrecent-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_history_recent-depression
    - cox_ipw-cohort_prevax_extf-sub_history_recent-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_history_recent-depression
    - cox_ipw-cohort_unvax_extf-sub_history_recent-serious_mental_illness
    - cox_ipw-cohort_vax-sub_history_recent-depression
    - cox_ipw-cohort_vax-sub_history_recent-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_sex_female-depression
    - cox_ipw-cohort_prevax_extf-sub_sex_female-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_sex_female-depression
    - cox_ipw-cohort_unvax_extf-sub_sex_female-serious_mental_illness
    - cox_ipw-cohort_vax-sub_sex_female-depression
    - cox_ipw-cohort_vax-sub_sex_female-serious_mental_illness
    - cox_ipw-cohort_prevax_extf-sub_sex_male-depression
    - cox_ipw-cohort_prevax_extf-sub_sex_male-serious_mental_illness
    - cox_ipw-cohort_unvax_extf-sub_sex_male-depression
    - cox_ipw-cohort_unvax_extf-sub_sex_male-serious_mental_illness
    - cox_ipw-cohort_vax-sub_sex_male-depression
    - cox_ipw-cohort_vax-sub_sex_male-serious_mental_illness
    outputs:
      moderately_sensitive:
        model_output: output/model_output.csv
        model_output_rounded: output/model_output_rounded.csv

  make_consort_output:
    run: r:latest analysis/make_other_output.R consort prevax_extf;vax;unvax_extf
    needs:
    - stage1_data_cleaning_prevax_extf
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax_extf
    outputs:
      moderately_sensitive:
        consort_output_rounded: output/consort_output_rounded.csv

  make_table1_output:
    run: r:latest analysis/make_other_output.R table1 prevax_extf;vax;unvax_extf
    needs:
    - table1_prevax_extf
    - table1_vax
    - table1_unvax_extf
    outputs:
      moderately_sensitive:
        table1_output_rounded: output/table1_output_rounded.csv

  make_extendedtable1_output:
    run: r:latest analysis/make_other_output.R extendedtable1 prevax_extf;vax;unvax_extf
    needs:
    - extendedtable1_prevax_extf
    - extendedtable1_vax
    - extendedtable1_unvax_extf
    outputs:
      moderately_sensitive:
        table1_output_rounded: output/extendedtable1_output_rounded.csv

  make_table2_output:
    run: r:latest analysis/make_other_output.R table2 prevax_extf;vax;unvax_extf
    needs:
    - table2_prevax_extf
    - table2_vax
    - table2_unvax_extf
    outputs:
      moderately_sensitive:
        table2_output_rounded: output/table2_output_rounded.csv

  make_venn_output:
    run: r:latest analysis/make_other_output.R venn prevax_extf;vax;unvax_extf
    needs:
    - venn_prevax_extf
    - venn_vax
    - venn_unvax_extf
    outputs:
      moderately_sensitive:
        venn_output_rounded: output/venn_output_rounded.csv

  ## Make absolute excess risk (AER) input 

  make_aer_input:
    run: r:latest analysis/make_aer_input.R
    needs:
    - make_model_input-cohort_prevax_extf-main-addiction
    - make_model_input-cohort_prevax_extf-main-anxiety_general
    - make_model_input-cohort_prevax_extf-main-anxiety_ptsd
    - make_model_input-cohort_prevax_extf-main-depression
    - make_model_input-cohort_prevax_extf-main-eating_disorders
    - make_model_input-cohort_prevax_extf-main-self_harm
    - make_model_input-cohort_prevax_extf-main-serious_mental_illness
    - make_model_input-cohort_prevax_extf-main-suicide
    - make_model_input-cohort_unvax_extf-main-addiction
    - make_model_input-cohort_unvax_extf-main-anxiety_general
    - make_model_input-cohort_unvax_extf-main-anxiety_ptsd
    - make_model_input-cohort_unvax_extf-main-depression
    - make_model_input-cohort_unvax_extf-main-eating_disorders
    - make_model_input-cohort_unvax_extf-main-self_harm
    - make_model_input-cohort_unvax_extf-main-serious_mental_illness
    - make_model_input-cohort_unvax_extf-main-suicide
    - make_model_input-cohort_vax-main-addiction
    - make_model_input-cohort_vax-main-anxiety_general
    - make_model_input-cohort_vax-main-anxiety_ptsd
    - make_model_input-cohort_vax-main-depression
    - make_model_input-cohort_vax-main-eating_disorders
    - make_model_input-cohort_vax-main-self_harm
    - make_model_input-cohort_vax-main-serious_mental_illness
    - make_model_input-cohort_vax-main-suicide
    outputs:
      moderately_sensitive:
        aer_input: output/aer_input-main.csv
        aer_input_rounded: output/aer_input-main-rounded.csv

  ## Calculate median (IQR) for age 

  median_iqr_age:
    run: r:latest analysis/median_iqr_age.R
    needs:
    - stage1_data_cleaning_prevax_extf
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax_extf
    outputs:
      moderately_sensitive:
        model_output: output/median_iqr_age.csv