Skip to content

Job request: 20410

Organisation:
University of Bristol
Workspace:
post-covid-neurodegenerative-extf
ID:
xbe7ryxc7mrsh3ga
View repo View project.yaml

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

  • Action:
    venn_prevax
    Status:
    Status: Succeeded
    Job identifier:
    plzqip3q6p644he5
  • Action:
    venn_unvax
    Status:
    Status: Succeeded
    Job identifier:
    v6o6zzgkke7dhftd
  • Action:
    venn_vax
    Status:
    Status: Succeeded
    Job identifier:
    5eannsub4jdzxwia

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 350000

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.gz
        vax_eligible_dates: output/vax_eligible_dates.csv.gz

  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 

  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 - unvax 

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

  ## Generate study population - vax 

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

  ## Preprocess data - prevax 

  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 - unvax 

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

  ## Preprocess data - vax 

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

  count_study_def_variables:
    run: r:latest analysis/descriptives/intitial_input_counts.R
    needs:
    - generate_study_population_prevax
    - generate_study_population_unvax
    - generate_study_population_vax
    - preprocess_data_prevax
    - preprocess_data_unvax
    - preprocess_data_vax
    outputs:
      moderately_sensitive:
        counts: output/study_counts_prepro.txt
        vax_summary: output/describe_prepro_vax.txt
        prevax_summary: output/describe_prepro_prevax.txt
        unvax_summary: output/describe_prepro_unvax.txt

  count_stage1_variables:
    run: r:latest analysis/descriptives/second_input_counts.R
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_unvax
    - stage1_data_cleaning_vax
    outputs:
      moderately_sensitive:
        counts: output/study_counts_stage1clean.txt
        vax_summary: output/describe_stage1clean_vax.txt
        prevax_summary: output/describe_stage1clean_prevax.txt
        unvax_summary: output/describe_stage1clean_unvax.txt

  ## Stage 1 - data cleaning - prevax 

  stage1_data_cleaning_prevax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R prevax
    needs:
    - vax_eligibility_inputs
    - preprocess_data_prevax
    outputs:
      moderately_sensitive:
        consort: output/consort_prevax.csv
        consort_rounded: output/consort_prevax_rounded.csv
        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_stage1.rds

  ## Stage 1 - data cleaning - unvax 

  stage1_data_cleaning_unvax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R unvax
    needs:
    - vax_eligibility_inputs
    - preprocess_data_unvax
    outputs:
      moderately_sensitive:
        consort: output/consort_unvax.csv
        consort_rounded: output/consort_unvax_rounded.csv
        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_stage1.rds

  ## Stage 1 - data cleaning - vax 

  stage1_data_cleaning_vax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R vax
    needs:
    - vax_eligibility_inputs
    - preprocess_data_vax
    outputs:
      moderately_sensitive:
        consort: output/consort_vax.csv
        consort_rounded: output/consort_vax_rounded.csv
        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_stage1.rds

  make_consort_output:
    run: r:latest analysis/model/make_other_output.R consort prevax;vax;unvax
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        consort_output_rounded: output/consort_output_rounded.csv

  ## Table 1 - prevax 

  table1_prevax:
    run: r:latest analysis/descriptives/table1.R prevax
    needs:
    - stage1_data_cleaning_prevax
    outputs:
      moderately_sensitive:
        table1: output/table1_prevax.csv
        table1_rounded: output/table1_prevax_rounded.csv

  ## Table 1 - unvax 

  table1_unvax:
    run: r:latest analysis/descriptives/table1.R unvax
    needs:
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        table1: output/table1_unvax.csv
        table1_rounded: output/table1_unvax_rounded.csv

  ## Table 1 - vax 

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

  ## 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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
      --study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia.csv

  make_model_input-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-sub_covid_nonhospitalised-alzheimer_disease.rds

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

  cox_ipw-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease:
    run: cox-ipw:v0.0.27 --df_input=model_input-cohort_vax-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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease.csv

  make_model_input-cohort_vax-sub_covid_nonhospitalised-any_dementia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-sub_covid_nonhospitalised-any_dementia.rds

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

  cox_ipw-cohort_vax-sub_covid_nonhospitalised-any_dementia:
    run: cox-ipw:v0.0.27 --df_input=model_input-cohort_vax-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_num_tc_hdl_ratio
      --cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
      --study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
      --episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-any_dementia.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_nonhospitalised-any_dementia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-any_dementia.csv

  make_model_input-cohort_vax-sub_covid_nonhospitalised-cognitive_impairment:
    run: r:latest