Job request: 15953

Organisation:: University of Bristol
Workspace:: post-covid-neurodegenerative
ID:: fckoquysnok7lg5z
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:

make_model_input-cohort_vax-sub_age_60_79-parkinson_disease

Status:

Status: Succeeded

Job identifier:

shg25b3cueg4xtqh
Action:

make_model_input-cohort_prevax-sub_age_60_79-migraine

Status:

Status: Succeeded

Job identifier:

nyobod6j3rpe6ymo
Action:

make_model_input-cohort_unvax-sub_age_60_79-parkinson_disease

Status:

Status: Succeeded

Job identifier:

jtevqbsjjwatlt2a
Action:

make_model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder

Status:

Status: Succeeded

Job identifier:

xrsnwmz2qdo3yqdv
Action:

make_model_input-cohort_unvax-sub_age_60_79-migraine

Status:

Status: Succeeded

Job identifier:

3qhwqg62wwyv27kb
Action:

make_model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder

Status:

Status: Succeeded

Job identifier:

rpch4baj5oitsf3n
Action:

describe_model_input-cohort_prevax-sub_age_60_79-migraine

Status:

Status: Succeeded

Job identifier:

yllv3a67w23wbeza
Action:

make_model_input-cohort_prevax-sub_age_60_79-cognitive_impairment

Status:

Status: Succeeded

Job identifier:

6az3fuznwgiaj7md
Action:

describe_model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder

Status:

Status: Succeeded

Job identifier:

fofcvmzjfj4yhkej
Action:

make_model_input-cohort_unvax-sub_age_60_79-cognitive_impairment

Status:

Status: Succeeded

Job identifier:

i3vm67qhshnjzrgi
Action:

make_model_input-cohort_prevax-sub_age_60_79-parkinson_disease

Status:

Status: Succeeded

Job identifier:

lq5ap3nhbq3aoo7u
Action:

make_model_input-cohort_unvax-sub_age_60_79-any_dementia

Status:

Status: Succeeded

Job identifier:

gjfrbyyao2q5yqqj
Action:

make_model_input-cohort_vax-sub_age_60_79-rem_sleep_disorder

Status:

Status: Succeeded

Job identifier:

kizv3lfqy74sttq6
Action:

make_model_input-cohort_vax-sub_age_60_79-migraine

Status:

Status: Succeeded

Job identifier:

56fni3pugkdpyti4
Action:

describe_model_input-cohort_prevax-sub_age_60_79-cognitive_impairment

Status:

Status: Succeeded

Job identifier:

2grmjiajwm5aeu7f
Action:

make_model_input-cohort_vax-sub_age_60_79-any_dementia

Status:

Status: Succeeded

Job identifier:

tvkkooy4cjlwa7ux
Action:

describe_model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder

Status:

Status: Succeeded

Job identifier:

74ostrtjft3pcouk
Action:

make_model_input-cohort_unvax-sub_age_60_79-alzheimer_disease

Status:

Status: Succeeded

Job identifier:

4xl7m2f2bz2y4plq
Action:

describe_model_input-cohort_unvax-sub_age_60_79-any_dementia

Status:

Status: Succeeded

Job identifier:

435u3ltfizcufq3t
Action:

make_model_input-cohort_prevax-sub_age_60_79-alzheimer_disease

Status:

Status: Succeeded

Job identifier:

cpxy5kfsu3wyy6bz
Action:

make_model_input-cohort_vax-sub_age_60_79-alzheimer_disease

Status:

Status: Succeeded

Job identifier:

mkngtbd62644i4by
Action:

describe_model_input-cohort_unvax-sub_age_60_79-parkinson_disease

Status:

Status: Succeeded

Job identifier:

mngvrlng7ntyu4yu
Action:

describe_model_input-cohort_prevax-sub_age_60_79-alzheimer_disease

Status:

Status: Succeeded

Job identifier:

m66gpkscx72z2ygl
Action:

make_model_input-cohort_vax-sub_age_60_79-cognitive_impairment

Status:

Status: Succeeded

Job identifier:

ldgg2ofy3kwxepa2
Action:

make_model_input-cohort_prevax-sub_age_60_79-any_dementia

Status:

Status: Succeeded

Job identifier:

w6mqsc5zwp4biavv
Action:

describe_model_input-cohort_unvax-sub_age_60_79-alzheimer_disease

Status:

Status: Succeeded

Job identifier:

z7vd6f3upsfd66es
Action:

describe_model_input-cohort_unvax-sub_age_60_79-cognitive_impairment

Status:

Status: Succeeded

Job identifier:

s2k225y7yznggsgx
Action:

describe_model_input-cohort_vax-sub_age_60_79-rem_sleep_disorder

Status:

Status: Succeeded

Job identifier:

qzwzvn7tqsttb2ax
Action:

describe_model_input-cohort_vax-sub_age_60_79-parkinson_disease

Status:

Status: Succeeded

Job identifier:

aaeg6qkppwdxlzqh
Action:

describe_model_input-cohort_unvax-sub_age_60_79-migraine

Status:

Status: Succeeded

Job identifier:

mselm7osyyicuyqr
Action:

describe_model_input-cohort_prevax-sub_age_60_79-parkinson_disease

Status:

Status: Succeeded

Job identifier:

6od4n6dgz37m2y26
Action:

describe_model_input-cohort_prevax-sub_age_60_79-any_dementia

Status:

Status: Succeeded

Job identifier:

rqrdskmmvfz6y7em
Action:

describe_model_input-cohort_vax-sub_age_60_79-migraine

Status:

Status: Succeeded

Job identifier:

ykgggnrrhd3dqmdd
Action:

describe_model_input-cohort_vax-sub_age_60_79-any_dementia

Status:

Status: Succeeded

Job identifier:

kajfuonfmxbmhxhr
Action:

describe_model_input-cohort_vax-sub_age_60_79-cognitive_impairment

Status:

Status: Succeeded

Job identifier:

jmuf5solcomqriqu
Action:

describe_model_input-cohort_vax-sub_age_60_79-alzheimer_disease

Status:

Status: Succeeded

Job identifier:

5yl2g6shfbpxia7q
Pipeline

Show project.yaml
version: '3.0'

expectations:

  population_size: 200000

actions:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  ## Stage 5 - Run models 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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