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Job request: 15886

Organisation:
University of Bristol
Workspace:
post-covid-neurodegenerative
ID:
kwy4va2qpc5j4jqo

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

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

Jobs

Pipeline

Show project.yaml
version: '3.0'

expectations:

  population_size: 200000

actions:

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

  vax_eligibility_inputs:
    run: r:latest analysis/metadates.R
    outputs:
      highly_sensitive:
        study_dates_json: output/study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

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

  generate_index_dates:
    run: r:latest analysis/prelim.R
    needs:
    - vax_eligibility_inputs
    - generate_study_population_prelim
    outputs:
      highly_sensitive:
        index_dates: output/index_dates.csv.gz

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

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

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

  preprocess_data_prevax:
    run: r:latest analysis/preprocess/preprocess_data.R prevax
    needs:
    - generate_index_dates
    - generate_study_population_prevax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_prevax_stage0.txt
        describe_venn: output/not-for-review/describe_venn_prevax.txt
      highly_sensitive:
        cohort: output/input_prevax.rds
        venn: output/venn_prevax.rds

  preprocess_data_vax:
    run: r:latest analysis/preprocess/preprocess_data.R vax
    needs:
    - generate_index_dates
    - generate_study_population_vax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_vax_stage0.txt
        descrive_venn: output/not-for-review/describe_venn_vax.txt
      highly_sensitive:
        cohort: output/input_vax.rds
        venn: output/venn_vax.rds

  preprocess_data_unvax:
    run: r:latest analysis/preprocess/preprocess_data.R unvax
    needs:
    - generate_index_dates
    - generate_study_population_unvax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_unvax_stage0.txt
        describe_venn: output/not-for-review/describe_venn_unvax.txt
      highly_sensitive:
        cohort: output/input_unvax.rds
        venn: output/venn_unvax.rds

  stage1_data_cleaning_prevax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R prevax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_prevax.csv
        QA_rules: output/review/descriptives/QA_summary_prevax.csv
        IE_criteria: output/review/descriptives/Cohort_flow_prevax.csv
        histograms: output/not-for-review/numeric_histograms_prevax.svg
      highly_sensitive:
        cohort: output/input_prevax_*.rds

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

  stage1_data_cleaning_unvax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R unvax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_unvax.csv
        QA_rules: output/review/descriptives/QA_summary_unvax.csv
        IE_criteria: output/review/descriptives/Cohort_flow_unvax.csv
        histograms: output/not-for-review/numeric_histograms_unvax.svg
      highly_sensitive:
        cohort: output/input_unvax_*.rds

  describe_file-input_prevax_stage1:
    run: r:latest analysis/describe_file.R input_prevax_stage1 rds
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_prevax_stage1.txt

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

  describe_file-input_unvax_stage1:
    run: r:latest analysis/describe_file.R input_unvax_stage1 rds
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-input_unvax_stage1.txt

  ## Stage 5 - Run models 

  make_model_input-cohort_prevax-main-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-alzheimer_disease.rds

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

  cox_ipw-cohort_prevax-main-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_prevax-main-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-alzheimer_disease.csv

  make_model_input-cohort_prevax-main-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-any_dementia.rds

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

  cox_ipw-cohort_prevax-main-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-any_dementia.csv
    needs:
    - make_model_input-cohort_prevax-main-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-any_dementia.csv

  make_model_input-cohort_prevax-main-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-cognitive_impairment.rds

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

  cox_ipw-cohort_prevax-main-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_prevax-main-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-cognitive_impairment.csv

  make_model_input-cohort_prevax-main-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-migraine.rds

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

  cox_ipw-cohort_prevax-main-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-migraine.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-migraine.csv
    needs:
    - make_model_input-cohort_prevax-main-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-migraine.csv

  make_model_input-cohort_prevax-main-motor_neurone_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-motor_neurone_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-motor_neurone_disease.rds

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

  cox_ipw-cohort_prevax-main-motor_neurone_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-motor_neurone_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-motor_neurone_disease.csv
    needs:
    - make_model_input-cohort_prevax-main-motor_neurone_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-motor_neurone_disease.csv

  make_model_input-cohort_prevax-main-multiple_sclerosis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-multiple_sclerosis
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-multiple_sclerosis.rds

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

  cox_ipw-cohort_prevax-main-multiple_sclerosis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-multiple_sclerosis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-multiple_sclerosis.csv
    needs:
    - make_model_input-cohort_prevax-main-multiple_sclerosis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-multiple_sclerosis.csv

  make_model_input-cohort_prevax-main-other_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-other_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-other_dementias.rds

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

  cox_ipw-cohort_prevax-main-other_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-other_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-other_dementias.csv
    needs:
    - make_model_input-cohort_prevax-main-other_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-other_dementias.csv

  make_model_input-cohort_prevax-main-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-parkinson_disease.rds

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

  cox_ipw-cohort_prevax-main-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-parkinson_disease.csv
    needs:
    - make_model_input-cohort_prevax-main-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-parkinson_disease.csv

  make_model_input-cohort_prevax-main-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-rem_sleep_disorder.rds

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

  cox_ipw-cohort_prevax-main-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_prevax-main-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-rem_sleep_disorder.csv

  make_model_input-cohort_prevax-main-restless_leg_syndrome:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-restless_leg_syndrome
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-restless_leg_syndrome.rds

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

  cox_ipw-cohort_prevax-main-restless_leg_syndrome:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-restless_leg_syndrome.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-restless_leg_syndrome.csv
    needs:
    - make_model_input-cohort_prevax-main-restless_leg_syndrome
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-restless_leg_syndrome.csv

  make_model_input-cohort_prevax-main-unspecified_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-unspecified_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-unspecified_dementias.rds

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

  cox_ipw-cohort_prevax-main-unspecified_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-unspecified_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-unspecified_dementias.csv
    needs:
    - make_model_input-cohort_prevax-main-unspecified_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-unspecified_dementias.csv

  make_model_input-cohort_prevax-main-vascular_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-vascular_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-vascular_dementia.rds

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

  cox_ipw-cohort_prevax-main-vascular_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-vascular_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-vascular_dementia.csv
    needs:
    - make_model_input-cohort_prevax-main-vascular_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-vascular_dementia.csv

  make_model_input-cohort_unvax-main-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-alzheimer_disease.rds

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

  cox_ipw-cohort_unvax-main-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_unvax-main-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-alzheimer_disease.csv

  make_model_input-cohort_unvax-main-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-any_dementia.rds

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

  cox_ipw-cohort_unvax-main-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-any_dementia.csv
    needs:
    - make_model_input-cohort_unvax-main-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-any_dementia.csv

  make_model_input-cohort_unvax-main-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-cognitive_impairment.rds

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

  cox_ipw-cohort_unvax-main-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_unvax-main-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-cognitive_impairment.csv

  make_model_input-cohort_unvax-main-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-migraine.rds

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

  cox_ipw-cohort_unvax-main-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-migraine.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-migraine.csv
    needs:
    - make_model_input-cohort_unvax-main-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-migraine.csv

  make_model_input-cohort_unvax-main-motor_neurone_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-motor_neurone_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-motor_neurone_disease.rds

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

  cox_ipw-cohort_unvax-main-motor_neurone_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-motor_neurone_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-motor_neurone_disease.csv
    needs:
    - make_model_input-cohort_unvax-main-motor_neurone_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-motor_neurone_disease.csv

  make_model_input-cohort_unvax-main-multiple_sclerosis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-multiple_sclerosis
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-multiple_sclerosis.rds

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

  cox_ipw-cohort_unvax-main-multiple_sclerosis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-multiple_sclerosis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-multiple_sclerosis.csv
    needs:
    - make_model_input-cohort_unvax-main-multiple_sclerosis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-multiple_sclerosis.csv

  make_model_input-cohort_unvax-main-other_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-other_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-other_dementias.rds

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

  cox_ipw-cohort_unvax-main-other_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-other_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-other_dementias.csv
    needs:
    - make_model_input-cohort_unvax-main-other_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-other_dementias.csv

  make_model_input-cohort_unvax-main-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-parkinson_disease.rds

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

  cox_ipw-cohort_unvax-main-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-parkinson_disease.csv
    needs:
    - make_model_input-cohort_unvax-main-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-parkinson_disease.csv

  make_model_input-cohort_unvax-main-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-rem_sleep_disorder.rds

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

  cox_ipw-cohort_unvax-main-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_unvax-main-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-rem_sleep_disorder.csv

  make_model_input-cohort_unvax-main-restless_leg_syndrome:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-restless_leg_syndrome
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-restless_leg_syndrome.rds

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

  cox_ipw-cohort_unvax-main-restless_leg_syndrome:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-restless_leg_syndrome.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-restless_leg_syndrome.csv
    needs:
    - make_model_input-cohort_unvax-main-restless_leg_syndrome
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-restless_leg_syndrome.csv

  make_model_input-cohort_unvax-main-unspecified_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-unspecified_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-unspecified_dementias.rds

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

  cox_ipw-cohort_unvax-main-unspecified_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-unspecified_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-unspecified_dementias.csv
    needs:
    - make_model_input-cohort_unvax-main-unspecified_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-unspecified_dementias.csv

  make_model_input-cohort_unvax-main-vascular_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-vascular_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-vascular_dementia.rds

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

  cox_ipw-cohort_unvax-main-vascular_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-vascular_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-vascular_dementia.csv
    needs:
    - make_model_input-cohort_unvax-main-vascular_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-vascular_dementia.csv

  make_model_input-cohort_vax-main-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-alzheimer_disease.rds

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

  cox_ipw-cohort_vax-main-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_vax-main-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-alzheimer_disease.csv

  make_model_input-cohort_vax-main-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-any_dementia.rds

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

  cox_ipw-cohort_vax-main-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-any_dementia.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-any_dementia.csv
    needs:
    - make_model_input-cohort_vax-main-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-any_dementia.csv

  make_model_input-cohort_vax-main-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-cognitive_impairment.rds

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

  cox_ipw-cohort_vax-main-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_vax-main-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-cognitive_impairment.csv

  make_model_input-cohort_vax-main-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-migraine.rds

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

  cox_ipw-cohort_vax-main-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-migraine.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-migraine.csv
    needs:
    - make_model_input-cohort_vax-main-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-migraine.csv

  make_model_input-cohort_vax-main-motor_neurone_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-motor_neurone_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-motor_neurone_disease.rds

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

  cox_ipw-cohort_vax-main-motor_neurone_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-motor_neurone_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-motor_neurone_disease.csv
    needs:
    - make_model_input-cohort_vax-main-motor_neurone_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-motor_neurone_disease.csv

  make_model_input-cohort_vax-main-multiple_sclerosis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-multiple_sclerosis
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-multiple_sclerosis.rds

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

  cox_ipw-cohort_vax-main-multiple_sclerosis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-multiple_sclerosis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-multiple_sclerosis.csv
    needs:
    - make_model_input-cohort_vax-main-multiple_sclerosis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-multiple_sclerosis.csv

  make_model_input-cohort_vax-main-other_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-other_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-other_dementias.rds

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

  cox_ipw-cohort_vax-main-other_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-other_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-other_dementias.csv
    needs:
    - make_model_input-cohort_vax-main-other_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-other_dementias.csv

  make_model_input-cohort_vax-main-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-parkinson_disease.rds

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

  cox_ipw-cohort_vax-main-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-parkinson_disease.csv
    needs:
    - make_model_input-cohort_vax-main-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-parkinson_disease.csv

  make_model_input-cohort_vax-main-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-rem_sleep_disorder.rds

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

  cox_ipw-cohort_vax-main-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_vax-main-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-rem_sleep_disorder.csv

  make_model_input-cohort_vax-main-restless_leg_syndrome:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-restless_leg_syndrome
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-restless_leg_syndrome.rds

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

  cox_ipw-cohort_vax-main-restless_leg_syndrome:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-restless_leg_syndrome.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-restless_leg_syndrome.csv
    needs:
    - make_model_input-cohort_vax-main-restless_leg_syndrome
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-restless_leg_syndrome.csv

  make_model_input-cohort_vax-main-unspecified_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-unspecified_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-unspecified_dementias.rds

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

  cox_ipw-cohort_vax-main-unspecified_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-unspecified_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-unspecified_dementias.csv
    needs:
    - make_model_input-cohort_vax-main-unspecified_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-unspecified_dementias.csv

  make_model_input-cohort_vax-main-vascular_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-vascular_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-vascular_dementia.rds

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

  cox_ipw-cohort_vax-main-vascular_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-vascular_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-vascular_dementia.csv
    needs:
    - make_model_input-cohort_vax-main-vascular_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-vascular_dementia.csv

  make_model_input-cohort_prevax-sub_age_18_39-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-alzheimer_disease.rds

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

  cox_ipw-cohort_prevax-sub_age_18_39-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-alzheimer_disease.csv

  make_model_input-cohort_prevax-sub_age_18_39-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-any_dementia.rds

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

  cox_ipw-cohort_prevax-sub_age_18_39-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-any_dementia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-any_dementia.csv

  make_model_input-cohort_prevax-sub_age_18_39-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-cognitive_impairment.rds

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

  cox_ipw-cohort_prevax-sub_age_18_39-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-cognitive_impairment.csv

  make_model_input-cohort_prevax-sub_age_18_39-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-migraine.rds

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

  cox_ipw-cohort_prevax-sub_age_18_39-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-migraine.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-migraine.csv

  make_model_input-cohort_prevax-sub_age_18_39-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-parkinson_disease.rds

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

  cox_ipw-cohort_prevax-sub_age_18_39-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-parkinson_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-parkinson_disease.csv

  make_model_input-cohort_prevax-sub_age_18_39-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-rem_sleep_disorder.rds

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

  cox_ipw-cohort_prevax-sub_age_18_39-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-rem_sleep_disorder.csv

  make_model_input-cohort_unvax-sub_age_18_39-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-alzheimer_disease.rds

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

  cox_ipw-cohort_unvax-sub_age_18_39-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-alzheimer_disease.csv

  make_model_input-cohort_unvax-sub_age_18_39-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-any_dementia.rds

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

  cox_ipw-cohort_unvax-sub_age_18_39-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-any_dementia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-any_dementia.csv

  make_model_input-cohort_unvax-sub_age_18_39-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-cognitive_impairment.rds

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

  cox_ipw-cohort_unvax-sub_age_18_39-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-cognitive_impairment.csv

  make_model_input-cohort_unvax-sub_age_18_39-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-migraine.rds

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

  cox_ipw-cohort_unvax-sub_age_18_39-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-migraine.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-migraine.csv

  make_model_input-cohort_unvax-sub_age_18_39-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-parkinson_disease.rds

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

  cox_ipw-cohort_unvax-sub_age_18_39-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-parkinson_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-parkinson_disease.csv

  make_model_input-cohort_unvax-sub_age_18_39-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-rem_sleep_disorder.rds

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

  cox_ipw-cohort_unvax-sub_age_18_39-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-rem_sleep_disorder.csv

  make_model_input-cohort_vax-sub_age_18_39-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-alzheimer_disease.rds

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

  cox_ipw-cohort_vax-sub_age_18_39-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-alzheimer_disease.csv

  make_model_input-cohort_vax-sub_age_18_39-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-any_dementia.rds

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

  cox_ipw-cohort_vax-sub_age_18_39-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-any_dementia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-any_dementia.csv

  make_model_input-cohort_vax-sub_age_18_39-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-cognitive_impairment.rds

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

  cox_ipw-cohort_vax-sub_age_18_39-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-cognitive_impairment.csv

  make_model_input-cohort_vax-sub_age_18_39-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-migraine.rds

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

  cox_ipw-cohort_vax-sub_age_18_39-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-migraine.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-migraine.csv

  make_model_input-cohort_vax-sub_age_18_39-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-parkinson_disease.rds

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

  cox_ipw-cohort_vax-sub_age_18_39-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-parkinson_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-parkinson_disease.csv

  make_model_input-cohort_vax-sub_age_18_39-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-rem_sleep_disorder.rds

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

  cox_ipw-cohort_vax-sub_age_18_39-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-rem_sleep_disorder.csv

  make_model_input-cohort_prevax-sub_age_40_59-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-alzheimer_disease.rds

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

  cox_ipw-cohort_prevax-sub_age_40_59-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-alzheimer_disease.csv

  make_model_input-cohort_prevax-sub_age_40_59-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-any_dementia.rds

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

  cox_ipw-cohort_prevax-sub_age_40_59-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-any_dementia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-any_dementia.csv

  make_model_input-cohort_prevax-sub_age_40_59-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-cognitive_impairment.rds

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

  cox_ipw-cohort_prevax-sub_age_40_59-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-cognitive_impairment.csv

  make_model_input-cohort_prevax-sub_age_40_59-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-migraine.rds

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

  cox_ipw-cohort_prevax-sub_age_40_59-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-migraine.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-migraine.csv

  make_model_input-cohort_prevax-sub_age_40_59-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-parkinson_disease.rds

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

  cox_ipw-cohort_prevax-sub_age_40_59-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-parkinson_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-parkinson_disease.csv

  make_model_input-cohort_prevax-sub_age_40_59-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-rem_sleep_disorder.rds

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

  cox_ipw-cohort_prevax-sub_age_40_59-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-rem_sleep_disorder.csv

  make_model_input-cohort_unvax-sub_age_40_59-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-alzheimer_disease.rds

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

  cox_ipw-cohort_unvax-sub_age_40_59-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-alzheimer_disease.csv

  make_model_input-cohort_unvax-sub_age_40_59-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-any_dementia.rds

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

  cox_ipw-cohort_unvax-sub_age_40_59-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-any_dementia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-any_dementia.csv

  make_model_input-cohort_unvax-sub_age_40_59-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-cognitive_impairment.rds

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

  cox_ipw-cohort_unvax-sub_age_40_59-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-cognitive_impairment.csv

  make_model_input-cohort_unvax-sub_age_40_59-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-migraine.rds

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

  cox_ipw-cohort_unvax-sub_age_40_59-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-migraine.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-migraine.csv

  make_model_input-cohort_unvax-sub_age_40_59-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-parkinson_disease.rds

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

  cox_ipw-cohort_unvax-sub_age_40_59-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-parkinson_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-parkinson_disease.csv

  make_model_input-cohort_unvax-sub_age_40_59-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-rem_sleep_disorder.rds

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

  cox_ipw-cohort_unvax-sub_age_40_59-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-rem_sleep_disorder.csv

  make_model_input-cohort_vax-sub_age_40_59-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-alzheimer_disease.rds

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

  cox_ipw-cohort_vax-sub_age_40_59-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-alzheimer_disease.csv

  make_model_input-cohort_vax-sub_age_40_59-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-any_dementia.rds

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

  cox_ipw-cohort_vax-sub_age_40_59-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-any_dementia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-any_dementia.csv

  make_model_input-cohort_vax-sub_age_40_59-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-cognitive_impairment.rds

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

  cox_ipw-cohort_vax-sub_age_40_59-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-cognitive_impairment.csv

  make_model_input-cohort_vax-sub_age_40_59-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-migraine.rds

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

  cox_ipw-cohort_vax-sub_age_40_59-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-migraine.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-migraine.csv

  make_model_input-cohort_vax-sub_age_40_59-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-parkinson_disease.rds

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

  cox_ipw-cohort_vax-sub_age_40_59-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-parkinson_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-parkinson_disease.csv

  make_model_input-cohort_vax-sub_age_40_59-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-rem_sleep_disorder.rds

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

  cox_ipw-cohort_vax-sub_age_40_59-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-rem_sleep_disorder.csv

  make_model_input-cohort_prevax-sub_age_60_79-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-alzheimer_disease.rds

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

  cox_ipw-cohort_prevax-sub_age_60_79-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-alzheimer_disease.csv

  make_model_input-cohort_prevax-sub_age_60_79-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-any_dementia.rds

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

  cox_ipw-cohort_prevax-sub_age_60_79-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-any_dementia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-any_dementia.csv

  make_model_input-cohort_prevax-sub_age_60_79-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-cognitive_impairment.rds

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

  cox_ipw-cohort_prevax-sub_age_60_79-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-cognitive_impairment.csv

  make_model_input-cohort_prevax-sub_age_60_79-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-migraine.rds

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

  cox_ipw-cohort_prevax-sub_age_60_79-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-migraine.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-migraine.csv

  make_model_input-cohort_prevax-sub_age_60_79-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-parkinson_disease.rds

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

  cox_ipw-cohort_prevax-sub_age_60_79-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-parkinson_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-parkinson_disease.csv

  make_model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder.rds

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

  cox_ipw-cohort_prevax-sub_age_60_79-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-rem_sleep_disorder.csv

  make_model_input-cohort_unvax-sub_age_60_79-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-alzheimer_disease.rds

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

  cox_ipw-cohort_unvax-sub_age_60_79-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-alzheimer_disease.csv

  make_model_input-cohort_unvax-sub_age_60_79-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-any_dementia.rds

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

  cox_ipw-cohort_unvax-sub_age_60_79-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-any_dementia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-any_dementia.csv

  make_model_input-cohort_unvax-sub_age_60_79-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-cognitive_impairment.rds

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

  cox_ipw-cohort_unvax-sub_age_60_79-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-cognitive_impairment.csv

  make_model_input-cohort_unvax-sub_age_60_79-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-migraine.rds

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

  cox_ipw-cohort_unvax-sub_age_60_79-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-migraine.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-migraine.csv

  make_model_input-cohort_unvax-sub_age_60_79-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-parkinson_disease.rds

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

  cox_ipw-cohort_unvax-sub_age_60_79-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-parkinson_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-parkinson_disease.csv

  make_model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder.rds

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

  cox_ipw-cohort_unvax-sub_age_60_79-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-rem_sleep_disorder.csv

  make_model_input-cohort_vax-sub_age_60_79-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-alzheimer_disease.rds

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

  cox_ipw-cohort_vax-sub_age_60_79-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-alzheimer_disease.csv

  make_model_input-cohort_vax-sub_age_60_79-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-any_dementia.rds

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

  cox_ipw-cohort_vax-sub_age_60_79-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-any_dementia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-any_dementia.csv

  make_model_input-cohort_vax-sub_age_60_79-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-cognitive_impairment.rds

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

  cox_ipw-cohort_vax-sub_age_60_79-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-cognitive_impairment.csv

  make_model_input-cohort_vax-sub_age_60_79-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-migraine.rds

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

  cox_ipw-cohort_vax-sub_age_60_79-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-migraine.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-migraine.csv

  make_model_input-cohort_vax-sub_age_60_79-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-parkinson_disease.rds

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

  cox_ipw-cohort_vax-sub_age_60_79-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-parkinson_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-parkinson_disease.csv

  make_model_input-cohort_vax-sub_age_60_79-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-rem_sleep_disorder.rds

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

  cox_ipw-cohort_vax-sub_age_60_79-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-rem_sleep_disorder.csv

  make_model_input-cohort_prevax-sub_age_80_110-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-alzheimer_disease.rds

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

  cox_ipw-cohort_prevax-sub_age_80_110-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-alzheimer_disease.csv

  make_model_input-cohort_prevax-sub_age_80_110-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-any_dementia.rds

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

  cox_ipw-cohort_prevax-sub_age_80_110-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-any_dementia.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-any_dementia.csv

  make_model_input-cohort_prevax-sub_age_80_110-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-cognitive_impairment.rds

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

  cox_ipw-cohort_prevax-sub_age_80_110-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-cognitive_impairment.csv

  make_model_input-cohort_prevax-sub_age_80_110-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-migraine.rds

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

  cox_ipw-cohort_prevax-sub_age_80_110-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-migraine.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-migraine.csv

  make_model_input-cohort_prevax-sub_age_80_110-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-parkinson_disease.rds

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

  cox_ipw-cohort_prevax-sub_age_80_110-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-parkinson_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-parkinson_disease.csv

  make_model_input-cohort_prevax-sub_age_80_110-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-rem_sleep_disorder.rds

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

  cox_ipw-cohort_prevax-sub_age_80_110-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-rem_sleep_disorder.csv

  make_model_input-cohort_unvax-sub_age_80_110-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-alzheimer_disease.rds

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

  cox_ipw-cohort_unvax-sub_age_80_110-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-alzheimer_disease.csv

  make_model_input-cohort_unvax-sub_age_80_110-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-any_dementia.rds

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

  cox_ipw-cohort_unvax-sub_age_80_110-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-any_dementia.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-any_dementia.csv

  make_model_input-cohort_unvax-sub_age_80_110-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-cognitive_impairment.rds

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

  cox_ipw-cohort_unvax-sub_age_80_110-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-cognitive_impairment.csv

  make_model_input-cohort_unvax-sub_age_80_110-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-migraine.rds

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

  cox_ipw-cohort_unvax-sub_age_80_110-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-migraine.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-migraine.csv

  make_model_input-cohort_unvax-sub_age_80_110-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-parkinson_disease.rds

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

  cox_ipw-cohort_unvax-sub_age_80_110-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-parkinson_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-parkinson_disease.csv

  make_model_input-cohort_unvax-sub_age_80_110-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-rem_sleep_disorder.rds

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

  cox_ipw-cohort_unvax-sub_age_80_110-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-rem_sleep_disorder.csv

  make_model_input-cohort_vax-sub_age_80_110-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-alzheimer_disease.rds

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

  cox_ipw-cohort_vax-sub_age_80_110-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-alzheimer_disease.csv

  make_model_input-cohort_vax-sub_age_80_110-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-any_dementia.rds

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

  cox_ipw-cohort_vax-sub_age_80_110-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-any_dementia.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-any_dementia.csv

  make_model_input-cohort_vax-sub_age_80_110-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-cognitive_impairment.rds

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

  cox_ipw-cohort_vax-sub_age_80_110-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-cognitive_impairment.csv

  make_model_input-cohort_vax-sub_age_80_110-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-migraine.rds

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

  cox_ipw-cohort_vax-sub_age_80_110-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-migraine.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-migraine.csv

  make_model_input-cohort_vax-sub_age_80_110-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-parkinson_disease.rds

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

  cox_ipw-cohort_vax-sub_age_80_110-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-parkinson_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-parkinson_disease.csv

  make_model_input-cohort_vax-sub_age_80_110-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-rem_sleep_disorder.rds

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

  cox_ipw-cohort_vax-sub_age_80_110-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-rem_sleep_disorder.csv

  make_model_input-cohort_unvax-sub_covid_history-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-alzheimer_disease.rds

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

  cox_ipw-cohort_unvax-sub_covid_history-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-alzheimer_disease.csv

  make_model_input-cohort_unvax-sub_covid_history-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-any_dementia.rds

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

  cox_ipw-cohort_unvax-sub_covid_history-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-any_dementia.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-any_dementia.csv

  make_model_input-cohort_unvax-sub_covid_history-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-cognitive_impairment.rds

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

  cox_ipw-cohort_unvax-sub_covid_history-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-cognitive_impairment.csv

  make_model_input-cohort_unvax-sub_covid_history-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-migraine.rds

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

  cox_ipw-cohort_unvax-sub_covid_history-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-migraine.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-migraine.csv

  make_model_input-cohort_unvax-sub_covid_history-motor_neurone_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-motor_neurone_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-motor_neurone_disease.rds

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

  cox_ipw-cohort_unvax-sub_covid_history-motor_neurone_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-motor_neurone_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-motor_neurone_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-motor_neurone_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-motor_neurone_disease.csv

  make_model_input-cohort_unvax-sub_covid_history-multiple_sclerosis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-multiple_sclerosis
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-multiple_sclerosis.rds

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

  cox_ipw-cohort_unvax-sub_covid_history-multiple_sclerosis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-multiple_sclerosis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-multiple_sclerosis.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-multiple_sclerosis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-multiple_sclerosis.csv

  make_model_input-cohort_unvax-sub_covid_history-other_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-other_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-other_dementias.rds

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

  cox_ipw-cohort_unvax-sub_covid_history-other_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-other_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-other_dementias.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-other_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-other_dementias.csv

  make_model_input-cohort_unvax-sub_covid_history-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-parkinson_disease.rds

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

  cox_ipw-cohort_unvax-sub_covid_history-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-parkinson_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-parkinson_disease.csv

  make_model_input-cohort_unvax-sub_covid_history-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-rem_sleep_disorder.rds

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

  cox_ipw-cohort_unvax-sub_covid_history-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-rem_sleep_disorder.csv

  make_model_input-cohort_unvax-sub_covid_history-restless_leg_syndrome:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-restless_leg_syndrome
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-restless_leg_syndrome.rds

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

  cox_ipw-cohort_unvax-sub_covid_history-restless_leg_syndrome:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-restless_leg_syndrome.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-restless_leg_syndrome.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-restless_leg_syndrome
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-restless_leg_syndrome.csv

  make_model_input-cohort_unvax-sub_covid_history-unspecified_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-unspecified_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-unspecified_dementias.rds

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

  cox_ipw-cohort_unvax-sub_covid_history-unspecified_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-unspecified_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-unspecified_dementias.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-unspecified_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-unspecified_dementias.csv

  make_model_input-cohort_unvax-sub_covid_history-vascular_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-vascular_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-vascular_dementia.rds

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

  cox_ipw-cohort_unvax-sub_covid_history-vascular_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-vascular_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-vascular_dementia.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-vascular_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-vascular_dementia.csv

  make_model_input-cohort_vax-sub_covid_history-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-alzheimer_disease.rds

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

  cox_ipw-cohort_vax-sub_covid_history-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-alzheimer_disease.csv

  make_model_input-cohort_vax-sub_covid_history-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-any_dementia.rds

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

  cox_ipw-cohort_vax-sub_covid_history-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-any_dementia.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-any_dementia.csv

  make_model_input-cohort_vax-sub_covid_history-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-cognitive_impairment.rds

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

  cox_ipw-cohort_vax-sub_covid_history-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-cognitive_impairment.csv

  make_model_input-cohort_vax-sub_covid_history-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-migraine.rds

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

  cox_ipw-cohort_vax-sub_covid_history-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-migraine.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-migraine.csv

  make_model_input-cohort_vax-sub_covid_history-motor_neurone_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-motor_neurone_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-motor_neurone_disease.rds

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

  cox_ipw-cohort_vax-sub_covid_history-motor_neurone_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-motor_neurone_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-motor_neurone_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-motor_neurone_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-motor_neurone_disease.csv

  make_model_input-cohort_vax-sub_covid_history-multiple_sclerosis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-multiple_sclerosis
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-multiple_sclerosis.rds

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

  cox_ipw-cohort_vax-sub_covid_history-multiple_sclerosis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-multiple_sclerosis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-multiple_sclerosis.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-multiple_sclerosis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-multiple_sclerosis.csv

  make_model_input-cohort_vax-sub_covid_history-other_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-other_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-other_dementias.rds

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

  cox_ipw-cohort_vax-sub_covid_history-other_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-other_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-other_dementias.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-other_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-other_dementias.csv

  make_model_input-cohort_vax-sub_covid_history-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-parkinson_disease.rds

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

  cox_ipw-cohort_vax-sub_covid_history-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-parkinson_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-parkinson_disease.csv

  make_model_input-cohort_vax-sub_covid_history-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-rem_sleep_disorder.rds

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

  cox_ipw-cohort_vax-sub_covid_history-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-rem_sleep_disorder.csv

  make_model_input-cohort_vax-sub_covid_history-restless_leg_syndrome:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-restless_leg_syndrome
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-restless_leg_syndrome.rds

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

  cox_ipw-cohort_vax-sub_covid_history-restless_leg_syndrome:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-restless_leg_syndrome.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-restless_leg_syndrome.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-restless_leg_syndrome
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-restless_leg_syndrome.csv

  make_model_input-cohort_vax-sub_covid_history-unspecified_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-unspecified_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-unspecified_dementias.rds

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

  cox_ipw-cohort_vax-sub_covid_history-unspecified_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-unspecified_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-unspecified_dementias.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-unspecified_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-unspecified_dementias.csv

  make_model_input-cohort_vax-sub_covid_history-vascular_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-vascular_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-vascular_dementia.rds

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

  cox_ipw-cohort_vax-sub_covid_history-vascular_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-vascular_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-vascular_dementia.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-vascular_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-vascular_dementia.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-alzheimer_disease.rds

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-alzheimer_disease.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-any_dementia.rds

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-any_dementia.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-any_dementia.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-cognitive_impairment.rds

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-cognitive_impairment.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-migraine.rds

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-migraine.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-migraine.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-motor_neurone_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease.rds

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-multiple_sclerosis
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis.rds

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-other_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-other_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-other_dementias.rds

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-other_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-other_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-other_dementias.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-other_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-other_dementias.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-parkinson_disease.rds

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-parkinson_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-parkinson_disease.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder.rds

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome.rds

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-unspecified_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-unspecified_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-unspecified_dementias.rds

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-unspecified_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-unspecified_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-unspecified_dementias.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-unspecified_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-unspecified_dementias.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-vascular_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-vascular_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-vascular_dementia.rds

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

  cox_ipw-cohort_prevax-sub_covid_hospitalised-vascular_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-vascular_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-vascular_dementia.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-vascular_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-vascular_dementia.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-alzheimer_disease.rds

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-alzheimer_disease.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-any_dementia.rds

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-any_dementia.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-any_dementia.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-cognitive_impairment.rds

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-cognitive_impairment.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-migraine.rds

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-migraine.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-migraine.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-motor_neurone_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease.rds

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-multiple_sclerosis
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis.rds

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-other_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-other_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-other_dementias.rds

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-other_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-other_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-other_dementias.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-other_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-other_dementias.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-parkinson_disease.rds

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-parkinson_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-parkinson_disease.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder.rds

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome.rds

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-unspecified_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-unspecified_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-unspecified_dementias.rds

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-unspecified_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-unspecified_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-unspecified_dementias.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-unspecified_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-unspecified_dementias.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-vascular_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-vascular_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-vascular_dementia.rds

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

  cox_ipw-cohort_unvax-sub_covid_hospitalised-vascular_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-vascular_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-vascular_dementia.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-vascular_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-vascular_dementia.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-alzheimer_disease.rds

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-alzheimer_disease.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-any_dementia.rds

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-any_dementia.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-any_dementia.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-cognitive_impairment.rds

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-cognitive_impairment.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-migraine.rds

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-migraine.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-migraine.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-motor_neurone_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-motor_neurone_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-motor_neurone_disease.rds

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-motor_neurone_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-motor_neurone_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-motor_neurone_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-motor_neurone_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-motor_neurone_disease.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-multiple_sclerosis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-multiple_sclerosis
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-multiple_sclerosis.rds

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-multiple_sclerosis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-multiple_sclerosis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-multiple_sclerosis.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-multiple_sclerosis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-multiple_sclerosis.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-other_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-other_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-other_dementias.rds

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-other_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-other_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-other_dementias.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-other_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-other_dementias.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-parkinson_disease.rds

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-parkinson_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-parkinson_disease.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder.rds

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-restless_leg_syndrome
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome.rds

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-unspecified_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-unspecified_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-unspecified_dementias.rds

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-unspecified_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-unspecified_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-unspecified_dementias.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-unspecified_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-unspecified_dementias.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-vascular_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-vascular_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-vascular_dementia.rds

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

  cox_ipw-cohort_vax-sub_covid_hospitalised-vascular_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-vascular_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-vascular_dementia.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-vascular_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-vascular_dementia.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease.rds

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-any_dementia.rds

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-any_dementia.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-any_dementia.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment.rds

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-migraine.rds

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-migraine.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-migraine.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease.rds

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis.rds

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-other_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-other_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-other_dementias.rds

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-other_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-other_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-other_dementias.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-other_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-other_dementias.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease.rds

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder.rds

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome.rds

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias.rds

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-vascular_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia.rds

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

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease.rds

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-any_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-any_dementia.rds

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-any_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-any_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-any_dementia.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-any_dementia.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment.rds

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-migraine:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-migraine
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-migraine.rds

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-migraine:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-migraine.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-migraine.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-migraine
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-migraine.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease.rds

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis.rds

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-other_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-other_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-other_dementias.rds

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-other_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-other_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-other_dementias.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-other_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-other_dementias.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-parkinson_disease
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease.rds

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder.rds

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome.rds

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias.rds

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-vascular_dementia
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia.rds

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

  cox_ipw-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-vascular_dementi