project.yaml

version: '3.0'

expectations:
  population_size: 2000

actions:

  generate_resource_by_age:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_resource_by_age --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_resource_by_age.csv.gz

  summarise_resource_by_age:
    run: r:latest analysis/00_resource_by_age_check.R
    needs: [generate_resource_by_age]
    outputs:
      moderately_sensitive:
        summary_table: output/diagnostics/resource_by_age_group/table_yearly_resource.csv
        summary_plot: output/diagnostics/resource_by_age_group/plot_yearly_resource.jpeg

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input.csv.gz

  generate_dummy_data:
    run: r:latest analysis/01_generate_dummy_data.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        dummy_data_admissions: output/dummy_data/dummy_data_admissions.csv.gz
        dummy_data_outpatient: output/dummy_data/dummy_data_outpatient.csv.gz
        dummy_data_gp: output/dummy_data/dummy_data_gp.csv.gz
        dummy_data_testing_negative: output/dummy_data/dummy_data_testing_negative.csv.gz
        dummy_data_testing_positive: output/dummy_data/dummy_data_testing_positive.csv.gz

  generate_admissions:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_admissions
        --index-date-range "2018-10-01 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
    dummy_data_file: output/dummy_data/dummy_data_admissions.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_admissions: output/data_weekly/input_admissions_20*.csv.gz

  generate_outpatient:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_20*.csv.gz

  generate_outpatient_TF_cardiology:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_cardiology
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_cardiology_20*.csv.gz

  generate_outpatient_TF_community_paediatrics:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_community_paediatrics
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_community_paediatrics_20*.csv.gz

  generate_outpatient_TF_dermatology:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_dermatology
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_dermatology_20*.csv.gz

  generate_outpatient_TF_dietetics:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_dietetics
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_dietetics_20*.csv.gz

  generate_outpatient_TF_endocrinology:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_endocrinology
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_endocrinology_20*.csv.gz

  generate_outpatient_TF_gastrointestinal:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_gastrointestinal
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_gastrointestinal_20*.csv.gz

  generate_outpatient_TF_general:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_general
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_general_20*.csv.gz

  generate_outpatient_TF_haematology:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_haematology
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_haematology_20*.csv.gz

  generate_outpatient_TF_immunology_and_allergy:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_immunology_and_allergy
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_immunology_and_allergy_20*.csv.gz

  generate_outpatient_TF_infectious_disease:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_infectious_disease
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_infectious_disease_20*.csv.gz

  generate_outpatient_TF_mental_health:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_mental_health
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_mental_health_20*.csv.gz

  generate_outpatient_TF_metabolic:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_metabolic
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_metabolic_20*.csv.gz

  generate_outpatient_TF_neurology:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_neurology
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_neurology_20*.csv.gz

  generate_outpatient_TF_occupational_therapy:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_occupational_therapy
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_occupational_therapy_20*.csv.gz

  generate_outpatient_TF_oncology:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_oncology
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_oncology_20*.csv.gz

  generate_outpatient_TF_pain_management_and_palliative_care:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_pain_management_and_palliative_care
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_pain_management_and_palliative_care_20*.csv.gz

  generate_outpatient_TF_physiology:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_physiology
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_physiology_20*.csv.gz

  generate_outpatient_TF_physiotherapy:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_physiotherapy
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_physiotherapy_20*.csv.gz

  generate_outpatient_TF_post_covid_clinic:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_post_covid_clinic
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_post_covid_clinic_20*.csv.gz

  generate_outpatient_TF_rehabilitation:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_rehabilitation
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_rehabilitation_20*.csv.gz

  generate_outpatient_TF_renal:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_renal
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_renal_20*.csv.gz

  generate_outpatient_TF_respiratory:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_respiratory
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_respiratory_20*.csv.gz

  generate_outpatient_TF_rheumatology:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_rheumatology
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_rheumatology_20*.csv.gz

  generate_outpatient_TF_speech_and_language_therapy:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient_TF_speech_and_language_therapy
        --index-date-range "2019-03-11 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_TF_speech_and_language_therapy_20*.csv.gz

  generate_covid_tests_negative:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_covid_tests_negative
        --index-date-range "2019-12-30 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
    dummy_data_file: output/dummy_data/dummy_data_testing_negative.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_negative_tests: output/data_weekly/input_covid_tests_negative_20*.csv.gz

  generate_covid_tests_positive:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_covid_tests_positive
        --index-date-range "2019-12-30 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
    dummy_data_file: output/dummy_data/dummy_data_testing_positive.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_positive_tests: output/data_weekly/input_covid_tests_positive_20*.csv.gz

  generate_gp_KM_auditory_system:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_auditory_system
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_auditory_system_20*.csv.gz

  generate_gp_KM_cardiovascular_system:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_cardiovascular_system
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_cardiovascular_system_20*.csv.gz

  generate_gp_KM_cellular_component_of_blood:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_cellular_component_of_blood
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_cellular_component_of_blood_20*.csv.gz

  generate_gp_KM_central_nervous_system:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_central_nervous_system
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_central_nervous_system_20*.csv.gz

  generate_gp_KM_congenital_disease:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_congenital_disease
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_congenital_disease_20*.csv.gz

  generate_gp_KM_connective_tissue:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_connective_tissue
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_connective_tissue_20*.csv.gz

  generate_gp_KM_digestive_system:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_digestive_system
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_digestive_system_20*.csv.gz

  generate_gp_KM_endocrine_system:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_endocrine_system
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_endocrine_system_20*.csv.gz

  generate_gp_KM_fetus_newborn:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_fetus_newborn
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_fetus_newborn_20*.csv.gz

  generate_gp_KM_genitourinary_system:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_genitourinary_system
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_genitourinary_system_20*.csv.gz

  generate_gp_KM_hematopoietic_structure:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_hematopoietic_structure
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_hematopoietic_structure_20*.csv.gz

  generate_gp_KM_immune_function:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_immune_function
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_immune_function_20*.csv.gz

  generate_gp_KM_infectious_disease:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_infectious_disease
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_infectious_disease_20*.csv.gz

  generate_gp_KM_labor_delivery:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_labor_delivery
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_labor_delivery_20*.csv.gz

  generate_gp_KM_mental_disorder:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_mental_disorder
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_mental_disorder_20*.csv.gz

  generate_gp_KM_metabolic_disease:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_metabolic_disease
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_metabolic_disease_20*.csv.gz

  generate_gp_KM_musculoskeletal_system:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_musculoskeletal_system
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_musculoskeletal_system_20*.csv.gz

  generate_gp_KM_neoplastic_disease:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_neoplastic_disease
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_neoplastic_disease_20*.csv.gz

  generate_gp_KM_nervous_system:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_nervous_system
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_nervous_system_20*.csv.gz

  generate_gp_KM_nutritional_disorder:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_nutritional_disorder
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_nutritional_disorder_20*.csv.gz

  generate_gp_KM_poisoning:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_poisoning
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_poisoning_20*.csv.gz

  generate_gp_KM_pregnancy_childbirth:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_pregnancy_childbirth
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_pregnancy_childbirth_20*.csv.gz

  generate_gp_KM_puerperium:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_puerperium
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_puerperium_20*.csv.gz

  generate_gp_KM_respiratory_system:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_respiratory_system
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_respiratory_system_20*.csv.gz

  generate_gp_KM_self_harm:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_self_harm
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_self_harm_20*.csv.gz

  generate_gp_KM_skin_subcutaneous_tissue:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_skin_subcutaneous_tissue
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_skin_subcutaneous_tissue_20*.csv.gz

  generate_gp_KM_traumatic_injury:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_traumatic_injury
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_traumatic_injury_20*.csv.gz

  generate_gp_KM_visual_system:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_KM_visual_system
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_KM_visual_system_20*.csv.gz

  generate_gp_mapped_0_occupations:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_mapped_0_occupations
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_mapped_0_occupations_20*.csv.gz

  generate_gp_mapped_1_history_symptoms:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_mapped_1_history_symptoms
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_mapped_1_history_symptoms_20*.csv.gz

  generate_gp_mapped_2_examination_signs:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_mapped_2_examination_signs
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_mapped_2_examination_signs_20*.csv.gz

  generate_gp_mapped_3_diagnostic_procedures:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_mapped_3_diagnostic_procedures
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_mapped_3_diagnostic_procedures_20*.csv.gz

  generate_gp_mapped_4_laboratory_procedures:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_mapped_4_laboratory_procedures
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_mapped_4_laboratory_procedures_20*.csv.gz

  generate_gp_mapped_5_radiology_physics_in_medicine:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_mapped_5_radiology_physics_in_medicine
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_mapped_5_radiology_physics_in_medicine_20*.csv.gz

  generate_gp_mapped_6_preventive_procedures:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_mapped_6_preventive_procedures
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_mapped_6_preventive_procedures_20*.csv.gz

  generate_gp_mapped_7_operations_procedures_sites:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_mapped_7_operations_procedures_sites
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_mapped_7_operations_procedures_sites_20*.csv.gz

  generate_gp_mapped_8_other_therapeutic_procedures:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_mapped_8_other_therapeutic_procedures
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_mapped_8_other_therapeutic_procedures_20*.csv.gz

  generate_gp_mapped_9_administration:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_mapped_9_administration
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_mapped_9_administration_20*.csv.gz

  process_patient_ids:
    run: r:latest analysis/02_process_patient_ids.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data_id: output/data/data_id.rds

  process_admissions_data:
    run: r:latest analysis/02_process_admissions_data.R
    needs: [generate_admissions, process_patient_ids]
    outputs:
      highly_sensitive:
        data_admissions: output/data/data_admissions.rds
      moderately_sensitive:
        diagnostics_admissions: output/diagnostics/diagnostics_admissions.csv

  process_gp_data:
    run: r:latest analysis/02_process_gp_data.R
    needs: [generate_gp_KM_auditory_system, generate_gp_KM_cardiovascular_system,
            generate_gp_KM_cellular_component_of_blood, generate_gp_KM_central_nervous_system,
            generate_gp_KM_congenital_disease, generate_gp_KM_connective_tissue,
            generate_gp_KM_digestive_system, generate_gp_KM_endocrine_system,
            generate_gp_KM_fetus_newborn, generate_gp_KM_genitourinary_system,
            generate_gp_KM_hematopoietic_structure, generate_gp_KM_immune_function,
            generate_gp_KM_infectious_disease, generate_gp_KM_labor_delivery,
            generate_gp_KM_mental_disorder, generate_gp_KM_metabolic_disease,
            generate_gp_KM_musculoskeletal_system, generate_gp_KM_neoplastic_disease,
            generate_gp_KM_nervous_system, generate_gp_KM_nutritional_disorder,
            generate_gp_KM_poisoning, generate_gp_KM_pregnancy_childbirth,
            generate_gp_KM_puerperium, generate_gp_KM_respiratory_system, generate_gp_KM_self_harm,
            generate_gp_KM_skin_subcutaneous_tissue, generate_gp_KM_traumatic_injury,
            generate_gp_KM_visual_system, 
            generate_gp_mapped_0_occupations, generate_gp_mapped_1_history_symptoms,
            generate_gp_mapped_2_examination_signs, generate_gp_mapped_3_diagnostic_procedures,
            generate_gp_mapped_4_laboratory_procedures, generate_gp_mapped_5_radiology_physics_in_medicine,
            generate_gp_mapped_6_preventive_procedures, generate_gp_mapped_7_operations_procedures_sites,
            generate_gp_mapped_8_other_therapeutic_procedures, generate_gp_mapped_9_administration,
            process_patient_ids]
    outputs:
      highly_sensitive:
        data_gp: output/data/data_gp.rds
      moderately_sensitive:
        diagnostics_gp: output/diagnostics/diagnostics_gp.csv

  process_outpatient_data:
    run: r:latest analysis/02_process_outpatient_data.R
    needs: [generate_outpatient,
            generate_outpatient_TF_cardiology, generate_outpatient_TF_community_paediatrics,
            generate_outpatient_TF_dermatology, generate_outpatient_TF_dietetics,
            generate_outpatient_TF_endocrinology, generate_outpatient_TF_gastrointestinal,
            generate_outpatient_TF_general, generate_outpatient_TF_haematology,
            generate_outpatient_TF_immunology_and_allergy, generate_outpatient_TF_infectious_disease,
            generate_outpatient_TF_mental_health, generate_outpatient_TF_metabolic,
            generate_outpatient_TF_neurology, generate_outpatient_TF_occupational_therapy,
            generate_outpatient_TF_oncology, generate_outpatient_TF_pain_management_and_palliative_care,
            generate_outpatient_TF_physiology, generate_outpatient_TF_physiotherapy,
            generate_outpatient_TF_post_covid_clinic, generate_outpatient_TF_rehabilitation,
            generate_outpatient_TF_renal, generate_outpatient_TF_respiratory,
            generate_outpatient_TF_rheumatology, generate_outpatient_TF_speech_and_language_therapy,
            process_patient_ids]
    outputs:
      highly_sensitive:
        data_outpatient: output/data/data_outpatient.rds
      moderately_sensitive:
        diagnostics_outpatient: output/diagnostics/diagnostics_outpatient.csv

  process_testing_data:
    run: r:latest analysis/02_process_testing_data.R
    needs: [generate_covid_tests_negative, generate_covid_tests_positive, process_patient_ids]
    outputs:
      highly_sensitive:
        data_testing: output/data/data_testing.rds
      moderately_sensitive:
        diagnostics_testing: output/diagnostics/diagnostics_testing.csv

  process_patient_data:
    run: r:latest analysis/02_process_patient_data.R
    needs: [generate_study_population, process_admissions_data, process_testing_data]
    outputs:
      highly_sensitive:
        data_patient: output/data/data_patient.rds

  summarise_datasets:
    run: r:latest analysis/03_summary_datasets.R
    needs: [process_patient_data, process_testing_data, process_admissions_data, process_outpatient_data, process_gp_data]
    outputs:
      moderately_sensitive:
        summary_datasets_tables: output/descriptives/summary_datasets/*.csv
        summary_datasets_plots: output/descriptives/summary_datasets/*.jpeg

  construct_yearly_cohort:
    run: r:latest analysis/05_construct_yearly_cohort.R
    needs: [process_patient_data]
    outputs:
      highly_sensitive:
        data_patient: output/data/data_cohort.rds
      moderately_sensitive:
        cohort_summary: output/descriptives/healthcare_use_2019_2022/tbl_cohort_summary.csv
        inclusion_flowchart: output/descriptives/healthcare_use_2019_2022/tbl_flowchart.csv

  comorbidity_regression_gp_negative_binomial:
    run: r:latest analysis/05_comorbidity_regression.R gp negative_binomial
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      highly_sensitive:
        model_fit: output/comorbidity_multivar/negative_binomial/gp/model/model_fit.rds
      moderately_sensitive:
        table_cohort_summary: output/comorbidity_multivar/negative_binomial/gp/tbl_cohort_summary.csv
        table_model_coef: output/comorbidity_multivar/negative_binomial/gp/tbl_model_coef.csv
        table_model_metrics: output/comorbidity_multivar/negative_binomial/gp/tbl_model_metrics.csv
        table_irr: output/comorbidity_multivar/negative_binomial/gp/tbl_irr.csv
        plot_model_coef_gp: output/comorbidity_multivar/negative_binomial/gp/plot_model_coef.jpeg

  comorbidity_regression_outpatient_negative_binomial:
    run: r:latest analysis/05_comorbidity_regression.R outpatient negative_binomial
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      highly_sensitive:
        model_fit: output/comorbidity_multivar/negative_binomial/outpatient/model/model_fit.rds
      moderately_sensitive:
        table_cohort_summary: output/comorbidity_multivar/negative_binomial/outpatient/tbl_cohort_summary.csv
        table_model_coef: output/comorbidity_multivar/negative_binomial/outpatient/tbl_model_coef.csv
        table_model_metrics: output/comorbidity_multivar/negative_binomial/outpatient/tbl_model_metrics.csv
        table_irr: output/comorbidity_multivar/negative_binomial/outpatient/tbl_irr.csv
        plot_model_coef_gp: output/comorbidity_multivar/negative_binomial/outpatient/plot_model_coef.jpeg

  comorbidity_regression_admissions_negative_binomial:
    run: r:latest analysis/05_comorbidity_regression.R admissions negative_binomial
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      highly_sensitive:
        model_fit: output/comorbidity_multivar/negative_binomial/admissions/model/model_fit.rds
      moderately_sensitive:
        table_cohort_summary: output/comorbidity_multivar/negative_binomial/admissions/tbl_cohort_summary.csv
        table_model_coef: output/comorbidity_multivar/negative_binomial/admissions/tbl_model_coef.csv
        table_model_metrics: output/comorbidity_multivar/negative_binomial/admissions/tbl_model_metrics.csv
        table_irr: output/comorbidity_multivar/negative_binomial/admissions/tbl_irr.csv
        plot_model_coef_gp: output/comorbidity_multivar/negative_binomial/admissions/plot_model_coef.jpeg

  comorbidity_regression_beddays_negative_binomial:
    run: r:latest analysis/05_comorbidity_regression.R beddays negative_binomial
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      highly_sensitive:
        model_fit: output/comorbidity_multivar/negative_binomial/beddays/model/model_fit.rds
      moderately_sensitive:
        table_cohort_summary: output/comorbidity_multivar/negative_binomial/beddays/tbl_cohort_summary.csv
        table_model_coef: output/comorbidity_multivar/negative_binomial/beddays/tbl_model_coef.csv
        table_model_metrics: output/comorbidity_multivar/negative_binomial/beddays/tbl_model_metrics.csv
        table_irr: output/comorbidity_multivar/negative_binomial/beddays/tbl_irr.csv
        plot_model_coef_gp: output/comorbidity_multivar/negative_binomial/beddays/plot_model_coef.jpeg

  summarise_comorbidity_regression_negative_binomial:
    run: r:latest analysis/05_comorbidity_regression_summary.R negative_binomial
    needs: [comorbidity_regression_gp_negative_binomial, comorbidity_regression_outpatient_negative_binomial,
            comorbidity_regression_admissions_negative_binomial, comorbidity_regression_beddays_negative_binomial]
    outputs:
      moderately_sensitive:
        tbl_irr_combined: output/comorbidity_multivar/negative_binomial/summary/tbl_irr_combined.csv
        plot_irr_combined: output/comorbidity_multivar/negative_binomial/summary/plot_irr_combined.jpeg

  monthly_gp_all_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp all overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_overall.jpeg

  monthly_gp_all_age_group:
    run: r:latest analysis/05_monthly_resource_use.R gp all age_group
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_age_group.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_age_group.jpeg

  monthly_gp_all_covid_status_tp:
    run: r:latest analysis/05_monthly_resource_use.R gp all covid_status_tp
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_covid_status_tp.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_covid_status_tp.jpeg

  monthly_gp_all_comorbidity_count_factor:
    run: r:latest analysis/05_monthly_resource_use.R gp all comorbidity_count_factor
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_comorbidity_count_factor.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_comorbidity_count_factor.jpeg

  monthly_gp_all_mental_health_disorders:
    run: r:latest analysis/05_monthly_resource_use.R gp all mental_health_disorders
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_mental_health_disorders.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_mental_health_disorders.jpeg

  monthly_gp_all_neurodevelopmental_and_behavioural:
    run: r:latest analysis/05_monthly_resource_use.R gp all neurodevelopmental_and_behavioural
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_neurodevelopmental_and_behavioural.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_neurodevelopmental_and_behavioural.jpeg

  monthly_gp_all_asthma:
    run: r:latest analysis/05_monthly_resource_use.R gp all asthma
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_asthma.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_asthma.jpeg

  monthly_gp_all_cystic_fibrosis:
    run: r:latest analysis/05_monthly_resource_use.R gp all cystic_fibrosis
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_cystic_fibrosis.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_cystic_fibrosis.jpeg

  monthly_gp_all_other_respiratory:
    run: r:latest analysis/05_monthly_resource_use.R gp all other_respiratory
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_other_respiratory.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_other_respiratory.jpeg

  monthly_gp_all_cardiovascular:
    run: r:latest analysis/05_monthly_resource_use.R gp all cardiovascular
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_cardiovascular.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_cardiovascular.jpeg

  monthly_gp_all_epilepsy:
    run: r:latest analysis/05_monthly_resource_use.R gp all epilepsy
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_epilepsy.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_epilepsy.jpeg

  monthly_gp_all_headaches:
    run: r:latest analysis/05_monthly_resource_use.R gp all headaches
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_headaches.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_headaches.jpeg

  monthly_gp_all_other_neurological:
    run: r:latest analysis/05_monthly_resource_use.R gp all other_neurological
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_other_neurological.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_other_neurological.jpeg

  monthly_gp_all_gastrointestinal_conditions:
    run: r:latest analysis/05_monthly_resource_use.R gp all gastrointestinal_conditions
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_gastrointestinal_conditions.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_gastrointestinal_conditions.jpeg

  monthly_gp_all_genitourinary:
    run: r:latest analysis/05_monthly_resource_use.R gp all genitourinary
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_genitourinary.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_genitourinary.jpeg

  monthly_gp_all_cancer:
    run: r:latest analysis/05_monthly_resource_use.R gp all cancer
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_cancer.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_cancer.jpeg

  monthly_gp_all_non_malignant_haematological:
    run: r:latest analysis/05_monthly_resource_use.R gp all non_malignant_haematological
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_non_malignant_haematological.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_non_malignant_haematological.jpeg

  monthly_gp_all_immunological:
    run: r:latest analysis/05_monthly_resource_use.R gp all immunological
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_immunological.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_immunological.jpeg

  monthly_gp_all_chronic_infections:
    run: r:latest analysis/05_monthly_resource_use.R gp all chronic_infections
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_chronic_infections.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_chronic_infections.jpeg

  monthly_gp_all_rheumatology:
    run: r:latest analysis/05_monthly_resource_use.R gp all rheumatology
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_rheumatology.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_rheumatology.jpeg

  monthly_gp_all_congenital_malformation:
    run: r:latest analysis/05_monthly_resource_use.R gp all congenital_malformation
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_congenital_malformation.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_congenital_malformation.jpeg

  monthly_gp_all_diabetes:
    run: r:latest analysis/05_monthly_resource_use.R gp all diabetes
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_diabetes.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_diabetes.jpeg

  monthly_gp_all_other_endocrine:
    run: r:latest analysis/05_monthly_resource_use.R gp all other_endocrine
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_other_endocrine.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_other_endocrine.jpeg

  monthly_gp_all_metabolic:
    run: r:latest analysis/05_monthly_resource_use.R gp all metabolic
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_metabolic.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_metabolic.jpeg

  monthly_gp_all_transplant:
    run: r:latest analysis/05_monthly_resource_use.R gp all transplant
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_transplant.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_transplant.jpeg

  monthly_gp_all_palliative_care:
    run: r:latest analysis/05_monthly_resource_use.R gp all palliative_care
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_palliative_care.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_palliative_care.jpeg

  monthly_gp_all_other_neurological_with_other_respiratory:
    run: r:latest analysis/05_monthly_resource_use.R gp all other_neurological_with_other_respiratory
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_other_neurological_with_other_respiratory.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_other_neurological_with_other_respiratory.jpeg

  monthly_gp_all_other_neurological_with_cardiovascular:
    run: r:latest analysis/05_monthly_resource_use.R gp all other_neurological_with_cardiovascular
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_other_neurological_with_cardiovascular.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_other_neurological_with_cardiovascular.jpeg

  monthly_gp_all_other_respiratory_with_cardiovascular:
    run: r:latest analysis/05_monthly_resource_use.R gp all other_respiratory_with_cardiovascular
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_all_other_respiratory_with_cardiovascular.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_all_other_respiratory_with_cardiovascular.jpeg


  monthly_gp_auditory_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp auditory_system overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_auditory_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_auditory_system_overall.jpeg

  monthly_gp_cardiovascular_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp cardiovascular_system overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_cardiovascular_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_cardiovascular_system_overall.jpeg

  monthly_gp_cellular_component_of_blood_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp cellular_component_of_blood overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_cellular_component_of_blood_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_cellular_component_of_blood_overall.jpeg

  monthly_gp_central_nervous_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp central_nervous_system overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_central_nervous_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_central_nervous_system_overall.jpeg

  monthly_gp_congenital_disease_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp congenital_disease overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_congenital_disease_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_congenital_disease_overall.jpeg

  monthly_gp_connective_tissue_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp connective_tissue overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_connective_tissue_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_connective_tissue_overall.jpeg

  monthly_gp_digestive_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp digestive_system overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_digestive_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_digestive_system_overall.jpeg

  monthly_gp_endocrine_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp endocrine_system overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_endocrine_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_endocrine_system_overall.jpeg

  monthly_gp_fetus_newborn_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp fetus_newborn overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_fetus_newborn_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_fetus_newborn_overall.jpeg

  monthly_gp_genitourinary_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp genitourinary_system overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_genitourinary_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_genitourinary_system_overall.jpeg

  monthly_gp_hematopoietic_structure_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp hematopoietic_structure overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_hematopoietic_structure_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_hematopoietic_structure_overall.jpeg

  monthly_gp_immune_function_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp immune_function overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_immune_function_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_immune_function_overall.jpeg

  monthly_gp_infectious_disease_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp infectious_disease overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_infectious_disease_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_infectious_disease_overall.jpeg

  monthly_gp_labor_delivery_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp labor_delivery overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_labor_delivery_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_labor_delivery_overall.jpeg

  monthly_gp_mental_disorder_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp mental_disorder overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_mental_disorder_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_mental_disorder_overall.jpeg

  monthly_gp_mental_disorder_age_group:
    run: r:latest analysis/05_monthly_resource_use.R gp mental_disorder age_group
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_mental_disorder_age_group.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_mental_disorder_age_group.jpeg

  monthly_gp_metabolic_disease_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp metabolic_disease overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_metabolic_disease_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_metabolic_disease_overall.jpeg

  monthly_gp_musculoskeletal_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp musculoskeletal_system overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_musculoskeletal_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_musculoskeletal_system_overall.jpeg

  monthly_gp_neoplastic_disease_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp neoplastic_disease overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_neoplastic_disease_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_neoplastic_disease_overall.jpeg

  monthly_gp_nervous_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp nervous_system overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_nervous_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_nervous_system_overall.jpeg

  monthly_gp_nutritional_disorder_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp nutritional_disorder overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_nutritional_disorder_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_nutritional_disorder_overall.jpeg

  monthly_gp_poisoning_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp poisoning overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_poisoning_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_poisoning_overall.jpeg

  monthly_gp_pregnancy_childbirth_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp pregnancy_childbirth overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_pregnancy_childbirth_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_pregnancy_childbirth_overall.jpeg

  monthly_gp_puerperium_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp puerperium overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_puerperium_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_puerperium_overall.jpeg

  monthly_gp_respiratory_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp respiratory_system overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_respiratory_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_respiratory_system_overall.jpeg

  monthly_gp_self_harm_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp self_harm overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_self_harm_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_self_harm_overall.jpeg

  monthly_gp_self_harm_age_group:
    run: r:latest analysis/05_monthly_resource_use.R gp self_harm age_group
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_self_harm_age_group.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_self_harm_age_group.jpeg

  monthly_gp_skin_subcutaneous_tissue_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp skin_subcutaneous_tissue overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_skin_subcutaneous_tissue_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_skin_subcutaneous_tissue_overall.jpeg

  monthly_gp_traumatic_injury_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp traumatic_injury overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_traumatic_injury_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_traumatic_injury_overall.jpeg

  monthly_gp_visual_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R gp visual_system overall
    needs: [construct_yearly_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_gp_visual_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_gp_visual_system_overall.jpeg

  monthly_outpatient_all_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_overall.jpeg

  monthly_outpatient_all_age_group:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all age_group
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_age_group.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_age_group.jpeg

  monthly_outpatient_all_covid_status_tp:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all covid_status_tp
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_covid_status_tp.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_covid_status_tp.jpeg

  monthly_outpatient_all_comorbidity_count_factor:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all comorbidity_count_factor
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_comorbidity_count_factor.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_comorbidity_count_factor.jpeg

  monthly_outpatient_all_mental_health_disorders:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all mental_health_disorders
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_mental_health_disorders.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_mental_health_disorders.jpeg

  monthly_outpatient_all_neurodevelopmental_and_behavioural:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all neurodevelopmental_and_behavioural
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_neurodevelopmental_and_behavioural.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_neurodevelopmental_and_behavioural.jpeg

  monthly_outpatient_all_asthma:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all asthma
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_asthma.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_asthma.jpeg

  monthly_outpatient_all_cystic_fibrosis:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all cystic_fibrosis
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_cystic_fibrosis.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_cystic_fibrosis.jpeg

  monthly_outpatient_all_other_respiratory:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all other_respiratory
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_other_respiratory.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_other_respiratory.jpeg

  monthly_outpatient_all_cardiovascular:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all cardiovascular
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_cardiovascular.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_cardiovascular.jpeg

  monthly_outpatient_all_epilepsy:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all epilepsy
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_epilepsy.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_epilepsy.jpeg

  monthly_outpatient_all_headaches:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all headaches
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_headaches.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_headaches.jpeg

  monthly_outpatient_all_other_neurological:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all other_neurological
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_other_neurological.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_other_neurological.jpeg

  monthly_outpatient_all_gastrointestinal_conditions:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all gastrointestinal_conditions
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_gastrointestinal_conditions.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_gastrointestinal_conditions.jpeg

  monthly_outpatient_all_genitourinary:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all genitourinary
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_genitourinary.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_genitourinary.jpeg

  monthly_outpatient_all_cancer:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all cancer
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_cancer.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_cancer.jpeg

  monthly_outpatient_all_non_malignant_haematological:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all non_malignant_haematological
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_non_malignant_haematological.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_non_malignant_haematological.jpeg

  monthly_outpatient_all_immunological:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all immunological
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_immunological.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_immunological.jpeg

  monthly_outpatient_all_chronic_infections:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all chronic_infections
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_chronic_infections.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_chronic_infections.jpeg

  monthly_outpatient_all_rheumatology:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all rheumatology
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_rheumatology.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_rheumatology.jpeg

  monthly_outpatient_all_congenital_malformation:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all congenital_malformation
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_congenital_malformation.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_congenital_malformation.jpeg

  monthly_outpatient_all_diabetes:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all diabetes
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_diabetes.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_diabetes.jpeg

  monthly_outpatient_all_other_endocrine:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all other_endocrine
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_other_endocrine.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_other_endocrine.jpeg

  monthly_outpatient_all_metabolic:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all metabolic
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_metabolic.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_metabolic.jpeg

  monthly_outpatient_all_transplant:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all transplant
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_transplant.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_transplant.jpeg

  monthly_outpatient_all_palliative_care:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all palliative_care
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_palliative_care.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_palliative_care.jpeg

  monthly_outpatient_all_other_neurological_with_other_respiratory:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all other_neurological_with_other_respiratory
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_other_neurological_with_other_respiratory.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_other_neurological_with_other_respiratory.jpeg

  monthly_outpatient_all_other_neurological_with_cardiovascular:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all other_neurological_with_cardiovascular
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_other_neurological_with_cardiovascular.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_other_neurological_with_cardiovascular.jpeg

  monthly_outpatient_all_other_respiratory_with_cardiovascular:
    run: r:latest analysis/05_monthly_resource_use.R outpatient all other_respiratory_with_cardiovascular
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_all_other_respiratory_with_cardiovascular.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_all_other_respiratory_with_cardiovascular.jpeg

  monthly_outpatient_cardiology_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient cardiology overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_cardiology_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_cardiology_overall.jpeg

  monthly_outpatient_community_paediatrics_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient community_paediatrics overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_community_paediatrics_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_community_paediatrics_overall.jpeg

  monthly_outpatient_dermatology_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient dermatology overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_dermatology_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_dermatology_overall.jpeg

  monthly_outpatient_dietetics_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient dietetics overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_dietetics_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_dietetics_overall.jpeg

  monthly_outpatient_endocrinology_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient endocrinology overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_endocrinology_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_endocrinology_overall.jpeg

  monthly_outpatient_gastrointestinal_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient gastrointestinal overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_gastrointestinal_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_gastrointestinal_overall.jpeg

  monthly_outpatient_general_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient general overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_general_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_general_overall.jpeg

  monthly_outpatient_haematology_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient haematology overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_haematology_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_haematology_overall.jpeg

  monthly_outpatient_immunology_and_allergy_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient immunology_and_allergy overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_immunology_and_allergy_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_immunology_and_allergy_overall.jpeg

  monthly_outpatient_infectious_disease_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient infectious_disease overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_infectious_disease_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_infectious_disease_overall.jpeg

  monthly_outpatient_mental_health_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient mental_health overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_mental_health_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_mental_health_overall.jpeg

  monthly_outpatient_mental_health_age_group:
    run: r:latest analysis/05_monthly_resource_use.R outpatient mental_health age_group
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_mental_health_age_group.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_mental_health_age_group.jpeg

  monthly_outpatient_metabolic_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient metabolic overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_metabolic_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_metabolic_overall.jpeg

  monthly_outpatient_neurology_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient neurology overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_neurology_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_neurology_overall.jpeg

  monthly_outpatient_occupational_therapy_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient occupational_therapy overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_occupational_therapy_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_occupational_therapy_overall.jpeg

  monthly_outpatient_oncology_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient oncology overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_oncology_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_oncology_overall.jpeg

  monthly_outpatient_pain_management_and_palliative_care_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient pain_management_and_palliative_care overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_pain_management_and_palliative_care_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_pain_management_and_palliative_care_overall.jpeg

  monthly_outpatient_physiology_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient physiology overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_physiology_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_physiology_overall.jpeg

  monthly_outpatient_physiotherapy_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient physiotherapy overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_physiotherapy_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_physiotherapy_overall.jpeg

  monthly_outpatient_post_covid_clinic_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient post_covid_clinic overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_post_covid_clinic_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_post_covid_clinic_overall.jpeg

  monthly_outpatient_rehabilitation_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient rehabilitation overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_rehabilitation_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_rehabilitation_overall.jpeg

  monthly_outpatient_renal_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient renal overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_renal_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_renal_overall.jpeg

  monthly_outpatient_respiratory_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient respiratory overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_respiratory_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_respiratory_overall.jpeg

  monthly_outpatient_rheumatology_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient rheumatology overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_rheumatology_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_rheumatology_overall.jpeg

  monthly_outpatient_speech_and_language_therapy_overall:
    run: r:latest analysis/05_monthly_resource_use.R outpatient speech_and_language_therapy overall
    needs: [construct_yearly_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_outpatient_speech_and_language_therapy_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_outpatient_speech_and_language_therapy_overall.jpeg

  monthly_admissions_all_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions all overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_overall.jpeg

  monthly_admissions_all_age_group:
    run: r:latest analysis/05_monthly_resource_use.R admissions all age_group
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_age_group.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_age_group.jpeg

  monthly_admissions_all_covid_status_tp:
    run: r:latest analysis/05_monthly_resource_use.R admissions all covid_status_tp
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_covid_status_tp.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_covid_status_tp.jpeg

  monthly_admissions_all_comorbidity_count_factor:
    run: r:latest analysis/05_monthly_resource_use.R admissions all comorbidity_count_factor
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_comorbidity_count_factor.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_comorbidity_count_factor.jpeg

  monthly_admissions_all_mental_health_disorders:
    run: r:latest analysis/05_monthly_resource_use.R admissions all mental_health_disorders
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_mental_health_disorders.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_mental_health_disorders.jpeg

  monthly_admissions_all_neurodevelopmental_and_behavioural:
    run: r:latest analysis/05_monthly_resource_use.R admissions all neurodevelopmental_and_behavioural
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_neurodevelopmental_and_behavioural.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_neurodevelopmental_and_behavioural.jpeg

  monthly_admissions_all_asthma:
    run: r:latest analysis/05_monthly_resource_use.R admissions all asthma
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_asthma.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_asthma.jpeg

  monthly_admissions_all_cystic_fibrosis:
    run: r:latest analysis/05_monthly_resource_use.R admissions all cystic_fibrosis
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_cystic_fibrosis.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_cystic_fibrosis.jpeg

  monthly_admissions_all_other_respiratory:
    run: r:latest analysis/05_monthly_resource_use.R admissions all other_respiratory
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_other_respiratory.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_other_respiratory.jpeg

  monthly_admissions_all_cardiovascular:
    run: r:latest analysis/05_monthly_resource_use.R admissions all cardiovascular
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_cardiovascular.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_cardiovascular.jpeg

  monthly_admissions_all_epilepsy:
    run: r:latest analysis/05_monthly_resource_use.R admissions all epilepsy
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_epilepsy.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_epilepsy.jpeg

  monthly_admissions_all_headaches:
    run: r:latest analysis/05_monthly_resource_use.R admissions all headaches
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_headaches.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_headaches.jpeg

  monthly_admissions_all_other_neurological:
    run: r:latest analysis/05_monthly_resource_use.R admissions all other_neurological
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_other_neurological.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_other_neurological.jpeg

  monthly_admissions_all_gastrointestinal_conditions:
    run: r:latest analysis/05_monthly_resource_use.R admissions all gastrointestinal_conditions
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_gastrointestinal_conditions.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_gastrointestinal_conditions.jpeg

  monthly_admissions_all_genitourinary:
    run: r:latest analysis/05_monthly_resource_use.R admissions all genitourinary
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_genitourinary.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_genitourinary.jpeg

  monthly_admissions_all_cancer:
    run: r:latest analysis/05_monthly_resource_use.R admissions all cancer
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_cancer.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_cancer.jpeg

  monthly_admissions_all_non_malignant_haematological:
    run: r:latest analysis/05_monthly_resource_use.R admissions all non_malignant_haematological
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_non_malignant_haematological.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_non_malignant_haematological.jpeg

  monthly_admissions_all_immunological:
    run: r:latest analysis/05_monthly_resource_use.R admissions all immunological
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_immunological.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_immunological.jpeg

  monthly_admissions_all_chronic_infections:
    run: r:latest analysis/05_monthly_resource_use.R admissions all chronic_infections
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_chronic_infections.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_chronic_infections.jpeg

  monthly_admissions_all_rheumatology:
    run: r:latest analysis/05_monthly_resource_use.R admissions all rheumatology
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_rheumatology.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_rheumatology.jpeg

  monthly_admissions_all_congenital_malformation:
    run: r:latest analysis/05_monthly_resource_use.R admissions all congenital_malformation
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_congenital_malformation.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_congenital_malformation.jpeg

  monthly_admissions_all_diabetes:
    run: r:latest analysis/05_monthly_resource_use.R admissions all diabetes
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_diabetes.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_diabetes.jpeg

  monthly_admissions_all_other_endocrine:
    run: r:latest analysis/05_monthly_resource_use.R admissions all other_endocrine
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_other_endocrine.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_other_endocrine.jpeg

  monthly_admissions_all_metabolic:
    run: r:latest analysis/05_monthly_resource_use.R admissions all metabolic
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_metabolic.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_metabolic.jpeg

  monthly_admissions_all_transplant:
    run: r:latest analysis/05_monthly_resource_use.R admissions all transplant
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_transplant.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_transplant.jpeg

  monthly_admissions_all_palliative_care:
    run: r:latest analysis/05_monthly_resource_use.R admissions all palliative_care
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_palliative_care.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_palliative_care.jpeg

  monthly_admissions_all_other_neurological_with_other_respiratory:
    run: r:latest analysis/05_monthly_resource_use.R admissions all other_neurological_with_other_respiratory
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_other_neurological_with_other_respiratory.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_other_neurological_with_other_respiratory.jpeg

  monthly_admissions_all_other_neurological_with_cardiovascular:
    run: r:latest analysis/05_monthly_resource_use.R admissions all other_neurological_with_cardiovascular
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_other_neurological_with_cardiovascular.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_other_neurological_with_cardiovascular.jpeg

  monthly_admissions_all_other_respiratory_with_cardiovascular:
    run: r:latest analysis/05_monthly_resource_use.R admissions all other_respiratory_with_cardiovascular
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_all_other_respiratory_with_cardiovascular.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_all_other_respiratory_with_cardiovascular.jpeg

  monthly_admissions_01_infectious_and_parasitic_diseases_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 01_infectious_and_parasitic_diseases overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_01_infectious_and_parasitic_diseases_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_01_infectious_and_parasitic_diseases_overall.jpeg

  monthly_admissions_02_neoplasms_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 02_neoplasms overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_02_neoplasms_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_02_neoplasms_overall.jpeg

  monthly_admissions_03_diseases_of_the_blood_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 03_diseases_of_the_blood overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_03_diseases_of_the_blood_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_03_diseases_of_the_blood_overall.jpeg

  monthly_admissions_04_endocrine_nutritional_and_metabolic_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 04_endocrine_nutritional_and_metabolic overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_04_endocrine_nutritional_and_metabolic_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_04_endocrine_nutritional_and_metabolic_overall.jpeg

  monthly_admissions_05_mental_and_behavioural_disorders_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 05_mental_and_behavioural_disorders overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_05_mental_and_behavioural_disorders_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_05_mental_and_behavioural_disorders_overall.jpeg

  monthly_admissions_05_mental_and_behavioural_disorders_age_group:
    run: r:latest analysis/05_monthly_resource_use.R admissions 05_mental_and_behavioural_disorders age_group
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_05_mental_and_behavioural_disorders_age_group.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_05_mental_and_behavioural_disorders_age_group.jpeg

  monthly_admissions_06_nervous_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 06_nervous_system overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_06_nervous_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_06_nervous_system_overall.jpeg

  monthly_admissions_07_eye_and_adnexa_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 07_eye_and_adnexa overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_07_eye_and_adnexa_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_07_eye_and_adnexa_overall.jpeg

  monthly_admissions_08_ear_and_mastoid_process_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 08_ear_and_mastoid_process overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_08_ear_and_mastoid_process_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_08_ear_and_mastoid_process_overall.jpeg

  monthly_admissions_09_circulatory_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 09_circulatory_system overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_09_circulatory_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_09_circulatory_system_overall.jpeg

  monthly_admissions_10_respiratory_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 10_respiratory_system overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_10_respiratory_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_10_respiratory_system_overall.jpeg

  monthly_admissions_11_digestive_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 11_digestive_system overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_11_digestive_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_11_digestive_system_overall.jpeg

  monthly_admissions_12_skin_and_subcutaneous_tissue_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 12_skin_and_subcutaneous_tissue overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_12_skin_and_subcutaneous_tissue_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_12_skin_and_subcutaneous_tissue_overall.jpeg

  monthly_admissions_13_musculoskeletal_and_connective_tissue_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 13_musculoskeletal_and_connective_tissue overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_13_musculoskeletal_and_connective_tissue_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_13_musculoskeletal_and_connective_tissue_overall.jpeg

  monthly_admissions_14_genitourinary_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 14_genitourinary_system overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_14_genitourinary_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_14_genitourinary_system_overall.jpeg

  monthly_admissions_15_pregnancy_childbirth_and_the_puerperium_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 15_pregnancy_childbirth_and_the_puerperium overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_15_pregnancy_childbirth_and_the_puerperium_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_15_pregnancy_childbirth_and_the_puerperium_overall.jpeg

  monthly_admissions_16_conditions_in_the_perinatal_period_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 16_conditions_in_the_perinatal_period overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_16_conditions_in_the_perinatal_period_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_16_conditions_in_the_perinatal_period_overall.jpeg

  monthly_admissions_17_congenital_malformations_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 17_congenital_malformations overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_17_congenital_malformations_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_17_congenital_malformations_overall.jpeg

  monthly_admissions_18_abnormal_clinical_and_laboratory_findings_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 18_abnormal_clinical_and_laboratory_findings overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_18_abnormal_clinical_and_laboratory_findings_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_18_abnormal_clinical_and_laboratory_findings_overall.jpeg

  monthly_admissions_19_injury_and_poisoning_excluding_poisoning_by_drugs_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 19_injury_and_poisoning_excluding_poisoning_by_drugs overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_19_injury_and_poisoning_excluding_poisoning_by_drugs_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_19_injury_and_poisoning_excluding_poisoning_by_drugs_overall.jpeg

  monthly_admissions_20_external_causes_excluding_self_harm_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 20_external_causes_excluding_self_harm overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_20_external_causes_excluding_self_harm_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_20_external_causes_excluding_self_harm_overall.jpeg

  monthly_admissions_21_factors_influencing_health_status_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 21_factors_influencing_health_status overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_21_factors_influencing_health_status_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_21_factors_influencing_health_status_overall.jpeg

  monthly_admissions_22_codes_for_special_purposes_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 22_codes_for_special_purposes overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_22_codes_for_special_purposes_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_22_codes_for_special_purposes_overall.jpeg

  monthly_admissions_23_self_harm_and_poisoning_by_drugs_overall:
    run: r:latest analysis/05_monthly_resource_use.R admissions 23_self_harm_and_poisoning_by_drugs overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_23_self_harm_and_poisoning_by_drugs_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_23_self_harm_and_poisoning_by_drugs_overall.jpeg

  monthly_admissions_23_self_harm_and_poisoning_by_drugs_age_group:
    run: r:latest analysis/05_monthly_resource_use.R admissions 23_self_harm_and_poisoning_by_drugs age_group
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_admissions_23_self_harm_and_poisoning_by_drugs_age_group.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_admissions_23_self_harm_and_poisoning_by_drugs_age_group.jpeg


  monthly_beddays_all_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays all overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_overall.jpeg

  monthly_beddays_all_age_group:
    run: r:latest analysis/05_monthly_resource_use.R beddays all age_group
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_age_group.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_age_group.jpeg

  monthly_beddays_all_covid_status_tp:
    run: r:latest analysis/05_monthly_resource_use.R beddays all covid_status_tp
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_covid_status_tp.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_covid_status_tp.jpeg

  monthly_beddays_all_comorbidity_count_factor:
    run: r:latest analysis/05_monthly_resource_use.R beddays all comorbidity_count_factor
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_comorbidity_count_factor.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_comorbidity_count_factor.jpeg

  monthly_beddays_all_mental_health_disorders:
    run: r:latest analysis/05_monthly_resource_use.R beddays all mental_health_disorders
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_mental_health_disorders.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_mental_health_disorders.jpeg

  monthly_beddays_all_neurodevelopmental_and_behavioural:
    run: r:latest analysis/05_monthly_resource_use.R beddays all neurodevelopmental_and_behavioural
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_neurodevelopmental_and_behavioural.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_neurodevelopmental_and_behavioural.jpeg

  monthly_beddays_all_asthma:
    run: r:latest analysis/05_monthly_resource_use.R beddays all asthma
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_asthma.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_asthma.jpeg

  monthly_beddays_all_cystic_fibrosis:
    run: r:latest analysis/05_monthly_resource_use.R beddays all cystic_fibrosis
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_cystic_fibrosis.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_cystic_fibrosis.jpeg

  monthly_beddays_all_other_respiratory:
    run: r:latest analysis/05_monthly_resource_use.R beddays all other_respiratory
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_other_respiratory.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_other_respiratory.jpeg

  monthly_beddays_all_cardiovascular:
    run: r:latest analysis/05_monthly_resource_use.R beddays all cardiovascular
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_cardiovascular.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_cardiovascular.jpeg

  monthly_beddays_all_epilepsy:
    run: r:latest analysis/05_monthly_resource_use.R beddays all epilepsy
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_epilepsy.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_epilepsy.jpeg

  monthly_beddays_all_headaches:
    run: r:latest analysis/05_monthly_resource_use.R beddays all headaches
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_headaches.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_headaches.jpeg

  monthly_beddays_all_other_neurological:
    run: r:latest analysis/05_monthly_resource_use.R beddays all other_neurological
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_other_neurological.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_other_neurological.jpeg

  monthly_beddays_all_gastrointestinal_conditions:
    run: r:latest analysis/05_monthly_resource_use.R beddays all gastrointestinal_conditions
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_gastrointestinal_conditions.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_gastrointestinal_conditions.jpeg

  monthly_beddays_all_genitourinary:
    run: r:latest analysis/05_monthly_resource_use.R beddays all genitourinary
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_genitourinary.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_genitourinary.jpeg

  monthly_beddays_all_cancer:
    run: r:latest analysis/05_monthly_resource_use.R beddays all cancer
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_cancer.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_cancer.jpeg

  monthly_beddays_all_non_malignant_haematological:
    run: r:latest analysis/05_monthly_resource_use.R beddays all non_malignant_haematological
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_non_malignant_haematological.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_non_malignant_haematological.jpeg

  monthly_beddays_all_immunological:
    run: r:latest analysis/05_monthly_resource_use.R beddays all immunological
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_immunological.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_immunological.jpeg

  monthly_beddays_all_chronic_infections:
    run: r:latest analysis/05_monthly_resource_use.R beddays all chronic_infections
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_chronic_infections.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_chronic_infections.jpeg

  monthly_beddays_all_rheumatology:
    run: r:latest analysis/05_monthly_resource_use.R beddays all rheumatology
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_rheumatology.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_rheumatology.jpeg

  monthly_beddays_all_congenital_malformation:
    run: r:latest analysis/05_monthly_resource_use.R beddays all congenital_malformation
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_congenital_malformation.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_congenital_malformation.jpeg

  monthly_beddays_all_diabetes:
    run: r:latest analysis/05_monthly_resource_use.R beddays all diabetes
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_diabetes.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_diabetes.jpeg

  monthly_beddays_all_other_endocrine:
    run: r:latest analysis/05_monthly_resource_use.R beddays all other_endocrine
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_other_endocrine.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_other_endocrine.jpeg

  monthly_beddays_all_metabolic:
    run: r:latest analysis/05_monthly_resource_use.R beddays all metabolic
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_metabolic.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_metabolic.jpeg

  monthly_beddays_all_transplant:
    run: r:latest analysis/05_monthly_resource_use.R beddays all transplant
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_transplant.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_transplant.jpeg

  monthly_beddays_all_palliative_care:
    run: r:latest analysis/05_monthly_resource_use.R beddays all palliative_care
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_palliative_care.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_palliative_care.jpeg

  monthly_beddays_all_other_neurological_with_other_respiratory:
    run: r:latest analysis/05_monthly_resource_use.R beddays all other_neurological_with_other_respiratory
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_other_neurological_with_other_respiratory.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_other_neurological_with_other_respiratory.jpeg

  monthly_beddays_all_other_neurological_with_cardiovascular:
    run: r:latest analysis/05_monthly_resource_use.R beddays all other_neurological_with_cardiovascular
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_other_neurological_with_cardiovascular.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_other_neurological_with_cardiovascular.jpeg

  monthly_beddays_all_other_respiratory_with_cardiovascular:
    run: r:latest analysis/05_monthly_resource_use.R beddays all other_respiratory_with_cardiovascular
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_all_other_respiratory_with_cardiovascular.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_all_other_respiratory_with_cardiovascular.jpeg

  monthly_beddays_01_infectious_and_parasitic_diseases_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 01_infectious_and_parasitic_diseases overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_01_infectious_and_parasitic_diseases_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_01_infectious_and_parasitic_diseases_overall.jpeg

  monthly_beddays_02_neoplasms_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 02_neoplasms overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_02_neoplasms_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_02_neoplasms_overall.jpeg

  monthly_beddays_03_diseases_of_the_blood_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 03_diseases_of_the_blood overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_03_diseases_of_the_blood_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_03_diseases_of_the_blood_overall.jpeg

  monthly_beddays_04_endocrine_nutritional_and_metabolic_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 04_endocrine_nutritional_and_metabolic overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_04_endocrine_nutritional_and_metabolic_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_04_endocrine_nutritional_and_metabolic_overall.jpeg

  monthly_beddays_05_mental_and_behavioural_disorders_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 05_mental_and_behavioural_disorders overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_05_mental_and_behavioural_disorders_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_05_mental_and_behavioural_disorders_overall.jpeg

  monthly_beddays_05_mental_and_behavioural_disorders_age_group:
    run: r:latest analysis/05_monthly_resource_use.R beddays 05_mental_and_behavioural_disorders age_group
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_05_mental_and_behavioural_disorders_age_group.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_05_mental_and_behavioural_disorders_age_group.jpeg

  monthly_beddays_06_nervous_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 06_nervous_system overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_06_nervous_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_06_nervous_system_overall.jpeg

  monthly_beddays_07_eye_and_adnexa_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 07_eye_and_adnexa overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_07_eye_and_adnexa_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_07_eye_and_adnexa_overall.jpeg

  monthly_beddays_08_ear_and_mastoid_process_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 08_ear_and_mastoid_process overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_08_ear_and_mastoid_process_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_08_ear_and_mastoid_process_overall.jpeg

  monthly_beddays_09_circulatory_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 09_circulatory_system overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_09_circulatory_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_09_circulatory_system_overall.jpeg

  monthly_beddays_10_respiratory_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 10_respiratory_system overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_10_respiratory_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_10_respiratory_system_overall.jpeg

  monthly_beddays_11_digestive_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 11_digestive_system overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_11_digestive_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_11_digestive_system_overall.jpeg

  monthly_beddays_12_skin_and_subcutaneous_tissue_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 12_skin_and_subcutaneous_tissue overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_12_skin_and_subcutaneous_tissue_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_12_skin_and_subcutaneous_tissue_overall.jpeg

  monthly_beddays_13_musculoskeletal_and_connective_tissue_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 13_musculoskeletal_and_connective_tissue overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_13_musculoskeletal_and_connective_tissue_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_13_musculoskeletal_and_connective_tissue_overall.jpeg

  monthly_beddays_14_genitourinary_system_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 14_genitourinary_system overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_14_genitourinary_system_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_14_genitourinary_system_overall.jpeg

  monthly_beddays_15_pregnancy_childbirth_and_the_puerperium_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 15_pregnancy_childbirth_and_the_puerperium overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_15_pregnancy_childbirth_and_the_puerperium_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_15_pregnancy_childbirth_and_the_puerperium_overall.jpeg

  monthly_beddays_16_conditions_in_the_perinatal_period_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 16_conditions_in_the_perinatal_period overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_16_conditions_in_the_perinatal_period_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_16_conditions_in_the_perinatal_period_overall.jpeg

  monthly_beddays_17_congenital_malformations_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 17_congenital_malformations overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_17_congenital_malformations_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_17_congenital_malformations_overall.jpeg

  monthly_beddays_18_abnormal_clinical_and_laboratory_findings_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 18_abnormal_clinical_and_laboratory_findings overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_18_abnormal_clinical_and_laboratory_findings_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_18_abnormal_clinical_and_laboratory_findings_overall.jpeg

  monthly_beddays_19_injury_and_poisoning_excluding_poisoning_by_drugs_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 19_injury_and_poisoning_excluding_poisoning_by_drugs overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_19_injury_and_poisoning_excluding_poisoning_by_drugs_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_19_injury_and_poisoning_excluding_poisoning_by_drugs_overall.jpeg

  monthly_beddays_20_external_causes_excluding_self_harm_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 20_external_causes_excluding_self_harm overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_20_external_causes_excluding_self_harm_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_20_external_causes_excluding_self_harm_overall.jpeg

  monthly_beddays_21_factors_influencing_health_status_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 21_factors_influencing_health_status overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_21_factors_influencing_health_status_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_21_factors_influencing_health_status_overall.jpeg

  monthly_beddays_22_codes_for_special_purposes_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 22_codes_for_special_purposes overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_22_codes_for_special_purposes_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_22_codes_for_special_purposes_overall.jpeg

  monthly_beddays_23_self_harm_and_poisoning_by_drugs_overall:
    run: r:latest analysis/05_monthly_resource_use.R beddays 23_self_harm_and_poisoning_by_drugs overall
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_23_self_harm_and_poisoning_by_drugs_overall.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_23_self_harm_and_poisoning_by_drugs_overall.jpeg

  monthly_beddays_23_self_harm_and_poisoning_by_drugs_age_group:
    run: r:latest analysis/05_monthly_resource_use.R beddays 23_self_harm_and_poisoning_by_drugs age_group
    needs: [construct_yearly_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        monthly_table: output/descriptives/healthcare_use_2019_2022/monthly_tables/monthly_beddays_23_self_harm_and_poisoning_by_drugs_age_group.csv
        monthly_plot: output/descriptives/healthcare_use_2019_2022/monthly_plots/monthly_beddays_23_self_harm_and_poisoning_by_drugs_age_group.jpeg


  summarise_monthly_resource_use:
    run: r:latest analysis/05_summarise_monthly_resource_use.R
    needs: [monthly_gp_all_overall, monthly_gp_all_age_group, monthly_gp_all_covid_status_tp,
            monthly_gp_all_comorbidity_count_factor, monthly_gp_all_mental_health_disorders,
            monthly_gp_all_neurodevelopmental_and_behavioural, monthly_gp_all_asthma,
            monthly_gp_all_cystic_fibrosis, monthly_gp_all_other_respiratory,
            monthly_gp_all_cardiovascular, monthly_gp_all_epilepsy, monthly_gp_all_headaches,
            monthly_gp_all_other_neurological, monthly_gp_all_gastrointestinal_conditions,
            monthly_gp_all_genitourinary, monthly_gp_all_cancer, monthly_gp_all_non_malignant_haematological,
            monthly_gp_all_immunological, monthly_gp_all_chronic_infections, 
            monthly_gp_all_rheumatology, monthly_gp_all_congenital_malformation,
            monthly_gp_all_diabetes, monthly_gp_all_other_endocrine, monthly_gp_all_metabolic,
            monthly_gp_all_transplant, monthly_gp_all_palliative_care,
            monthly_gp_all_other_neurological_with_other_respiratory,
            monthly_gp_all_other_neurological_with_cardiovascular,
            monthly_gp_all_other_respiratory_with_cardiovascular,
            monthly_gp_auditory_system_overall, monthly_gp_cardiovascular_system_overall,
            monthly_gp_cellular_component_of_blood_overall, monthly_gp_central_nervous_system_overall,
            monthly_gp_congenital_disease_overall, monthly_gp_connective_tissue_overall,
            monthly_gp_digestive_system_overall, monthly_gp_endocrine_system_overall,
            monthly_gp_fetus_newborn_overall, monthly_gp_genitourinary_system_overall,
            monthly_gp_hematopoietic_structure_overall, monthly_gp_immune_function_overall,
            monthly_gp_infectious_disease_overall, monthly_gp_labor_delivery_overall,
            monthly_gp_mental_disorder_overall, monthly_gp_mental_disorder_age_group,
            monthly_gp_metabolic_disease_overall, monthly_gp_musculoskeletal_system_overall,
            monthly_gp_neoplastic_disease_overall, monthly_gp_nervous_system_overall,
            monthly_gp_nutritional_disorder_overall, monthly_gp_poisoning_overall,
            monthly_gp_pregnancy_childbirth_overall, monthly_gp_puerperium_overall,
            monthly_gp_respiratory_system_overall, monthly_gp_self_harm_overall,
            monthly_gp_self_harm_age_group,
            monthly_gp_skin_subcutaneous_tissue_overall, monthly_gp_traumatic_injury_overall,
            monthly_gp_visual_system_overall, monthly_outpatient_all_overall,
            monthly_outpatient_all_age_group, monthly_outpatient_all_covid_status_tp,
            monthly_outpatient_all_comorbidity_count_factor, monthly_outpatient_all_mental_health_disorders,
            monthly_outpatient_all_neurodevelopmental_and_behavioural, monthly_outpatient_all_asthma,
            monthly_outpatient_all_cystic_fibrosis, monthly_outpatient_all_other_respiratory,
            monthly_outpatient_all_cardiovascular, monthly_outpatient_all_epilepsy,
            monthly_outpatient_all_headaches, monthly_outpatient_all_other_neurological,
            monthly_outpatient_all_gastrointestinal_conditions, monthly_outpatient_all_genitourinary,
            monthly_outpatient_all_cancer, monthly_outpatient_all_non_malignant_haematological,
            monthly_outpatient_all_immunological, monthly_outpatient_all_chronic_infections,
            monthly_outpatient_all_rheumatology, monthly_outpatient_all_congenital_malformation,
            monthly_outpatient_all_diabetes, monthly_outpatient_all_other_endocrine,
            monthly_outpatient_all_metabolic, monthly_outpatient_all_transplant,
            monthly_outpatient_all_palliative_care, 
            monthly_outpatient_all_other_neurological_with_other_respiratory,
            monthly_outpatient_all_other_neurological_with_cardiovascular,
            monthly_outpatient_all_other_respiratory_with_cardiovascular,
            monthly_outpatient_cardiology_overall, monthly_outpatient_community_paediatrics_overall,
            monthly_outpatient_dermatology_overall, monthly_outpatient_dietetics_overall,
            monthly_outpatient_endocrinology_overall, monthly_outpatient_gastrointestinal_overall,
            monthly_outpatient_general_overall, monthly_outpatient_haematology_overall,
            monthly_outpatient_immunology_and_allergy_overall, monthly_outpatient_infectious_disease_overall,
            monthly_outpatient_mental_health_overall, monthly_outpatient_mental_health_age_group,
            monthly_outpatient_metabolic_overall, monthly_outpatient_neurology_overall,
            monthly_outpatient_occupational_therapy_overall, monthly_outpatient_oncology_overall,
            monthly_outpatient_pain_management_and_palliative_care_overall,
            monthly_outpatient_physiology_overall, monthly_outpatient_physiotherapy_overall,
            monthly_outpatient_post_covid_clinic_overall, monthly_outpatient_rehabilitation_overall,
            monthly_outpatient_renal_overall, monthly_outpatient_respiratory_overall,
            monthly_outpatient_rheumatology_overall, monthly_outpatient_speech_and_language_therapy_overall,
            monthly_admissions_all_overall, monthly_admissions_all_age_group,
            monthly_admissions_all_covid_status_tp, monthly_admissions_all_comorbidity_count_factor,
            monthly_admissions_all_mental_health_disorders,
            monthly_admissions_all_neurodevelopmental_and_behavioural, monthly_admissions_all_asthma,
            monthly_admissions_all_cystic_fibrosis, monthly_admissions_all_other_respiratory,
            monthly_admissions_all_cardiovascular, monthly_admissions_all_epilepsy,
            monthly_admissions_all_headaches, monthly_admissions_all_other_neurological,
            monthly_admissions_all_gastrointestinal_conditions,
            monthly_admissions_all_genitourinary, monthly_admissions_all_cancer,
            monthly_admissions_all_non_malignant_haematological, monthly_admissions_all_immunological,
            monthly_admissions_all_chronic_infections, monthly_admissions_all_rheumatology,
            monthly_admissions_all_congenital_malformation, monthly_admissions_all_diabetes,
            monthly_admissions_all_other_endocrine, monthly_admissions_all_metabolic,
            monthly_admissions_all_transplant, monthly_admissions_all_palliative_care,
            monthly_admissions_all_other_neurological_with_other_respiratory,
            monthly_admissions_all_other_neurological_with_cardiovascular,
            monthly_admissions_all_other_respiratory_with_cardiovascular,
            monthly_admissions_01_infectious_and_parasitic_diseases_overall,
            monthly_admissions_02_neoplasms_overall,
            monthly_admissions_03_diseases_of_the_blood_overall,
            monthly_admissions_04_endocrine_nutritional_and_metabolic_overall,
            monthly_admissions_05_mental_and_behavioural_disorders_overall,
            monthly_admissions_05_mental_and_behavioural_disorders_age_group,
            monthly_admissions_06_nervous_system_overall,
            monthly_admissions_07_eye_and_adnexa_overall,
            monthly_admissions_08_ear_and_mastoid_process_overall,
            monthly_admissions_09_circulatory_system_overall,
            monthly_admissions_10_respiratory_system_overall,
            monthly_admissions_11_digestive_system_overall,
            monthly_admissions_12_skin_and_subcutaneous_tissue_overall,
            monthly_admissions_13_musculoskeletal_and_connective_tissue_overall,
            monthly_admissions_14_genitourinary_system_overall,
            monthly_admissions_15_pregnancy_childbirth_and_the_puerperium_overall,
            monthly_admissions_16_conditions_in_the_perinatal_period_overall,
            monthly_admissions_17_congenital_malformations_overall,
            monthly_admissions_18_abnormal_clinical_and_laboratory_findings_overall,
            monthly_admissions_19_injury_and_poisoning_excluding_poisoning_by_drugs_overall,
            monthly_admissions_20_external_causes_excluding_self_harm_overall,
            monthly_admissions_21_factors_influencing_health_status_overall,
            monthly_admissions_22_codes_for_special_purposes_overall,
            monthly_admissions_23_self_harm_and_poisoning_by_drugs_overall,
            monthly_admissions_23_self_harm_and_poisoning_by_drugs_age_group,
            monthly_beddays_all_overall, monthly_beddays_all_age_group,
            monthly_beddays_all_covid_status_tp, monthly_beddays_all_comorbidity_count_factor,
            monthly_beddays_all_mental_health_disorders, monthly_beddays_all_neurodevelopmental_and_behavioural,
            monthly_beddays_all_asthma, monthly_beddays_all_cystic_fibrosis,
            monthly_beddays_all_other_respiratory, monthly_beddays_all_cardiovascular,
            monthly_beddays_all_epilepsy, monthly_beddays_all_headaches,
            monthly_beddays_all_other_neurological, monthly_beddays_all_gastrointestinal_conditions,
            monthly_beddays_all_genitourinary, monthly_beddays_all_cancer,
            monthly_beddays_all_non_malignant_haematological, monthly_beddays_all_immunological,
            monthly_beddays_all_chronic_infections, monthly_beddays_all_rheumatology,
            monthly_beddays_all_congenital_malformation, monthly_beddays_all_diabetes,
            monthly_beddays_all_other_endocrine, monthly_beddays_all_metabolic,
            monthly_beddays_all_transplant, monthly_beddays_all_palliative_care,
            monthly_beddays_all_other_neurological_with_other_respiratory,
            monthly_beddays_all_other_neurological_with_cardiovascular,
            monthly_beddays_all_other_respiratory_with_cardiovascular,
            monthly_beddays_01_infectious_and_parasitic_diseases_overall,
            monthly_beddays_02_neoplasms_overall,
            monthly_beddays_03_diseases_of_the_blood_overall,
            monthly_beddays_04_endocrine_nutritional_and_metabolic_overall,
            monthly_beddays_05_mental_and_behavioural_disorders_overall,
            monthly_beddays_05_mental_and_behavioural_disorders_age_group,
            monthly_beddays_06_nervous_system_overall,
            monthly_beddays_07_eye_and_adnexa_overall,
            monthly_beddays_08_ear_and_mastoid_process_overall,
            monthly_beddays_09_circulatory_system_overall,
            monthly_beddays_10_respiratory_system_overall,
            monthly_beddays_11_digestive_system_overall,
            monthly_beddays_12_skin_and_subcutaneous_tissue_overall,
            monthly_beddays_13_musculoskeletal_and_connective_tissue_overall,
            monthly_beddays_14_genitourinary_system_overall,
            monthly_beddays_15_pregnancy_childbirth_and_the_puerperium_overall,
            monthly_beddays_16_conditions_in_the_perinatal_period_overall,
            monthly_beddays_17_congenital_malformations_overall,
            monthly_beddays_18_abnormal_clinical_and_laboratory_findings_overall,
            monthly_beddays_19_injury_and_poisoning_excluding_poisoning_by_drugs_overall,
            monthly_beddays_20_external_causes_excluding_self_harm_overall,
            monthly_beddays_21_factors_influencing_health_status_overall,
            monthly_beddays_22_codes_for_special_purposes_overall,
            monthly_beddays_23_self_harm_and_poisoning_by_drugs_overall,
            monthly_beddays_23_self_harm_and_poisoning_by_drugs_age_group]
    outputs:
      moderately_sensitive:
        monthly_resource_use: output/descriptives/healthcare_use_2019_2022/tbl_monthly_count_summarised.csv

  create_matched_cohort:
    run: r:latest analysis/06_matched_cohort.R
    needs: [process_patient_data, process_testing_data, process_admissions_data]
    outputs:
      highly_sensitive:
        data_matched: output/data/data_matched.rds
      moderately_sensitive:
        create_matched_cohort_tables: output/descriptives/matched_cohort/*.csv

  weight_matched_cohort:
    run: r:latest analysis/07_ipw.R
    needs: [process_patient_data, process_testing_data, process_admissions_data,
            process_outpatient_data, process_gp_data, create_matched_cohort]
    outputs:
      highly_sensitive:
        data_matched: output/data/data_weighted.rds
      moderately_sensitive:
        plot_followup: output/descriptives/matched_cohort/persontime/plot_followup_distribution.jpeg
        tbl_followup: output/descriptives/matched_cohort/persontime/tbl_followup_stats.csv
        summary_unweighted: output/descriptives/matched_cohort/ipw/summary_unweighted.csv
        effective_sample_size: output/descriptives/matched_cohort/ipw/table_effective_sample_size.csv
        table_pairwise_balance: output/descriptives/matched_cohort/ipw/table_pair_balance.csv
        table_balance_summmary: output/descriptives/matched_cohort/ipw/table_balance_summmary.csv
        balance_plots: output/descriptives/matched_cohort/ipw/balance_plot/*.jpeg
        love_plot: output/descriptives/matched_cohort/ipw/love_plot.jpeg

  count_regression_admissions_all_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions all poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_all.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_all.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_all.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_all.jpeg


  count_regression_admissions_01_infectious_and_parasitic_diseases_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions 01_infectious_and_parasitic_diseases poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_01_infectious_and_parasitic_diseases.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_01_infectious_and_parasitic_diseases.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_01_infectious_and_parasitic_diseases.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_01_infectious_and_parasitic_diseases.jpeg

  count_regression_admissions_02_neoplasms_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions 02_neoplasms poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_02_neoplasms.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_02_neoplasms.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_02_neoplasms.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_02_neoplasms.jpeg

  count_regression_admissions_03_diseases_of_the_blood_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions 03_diseases_of_the_blood poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_03_diseases_of_the_blood.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_03_diseases_of_the_blood.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_03_diseases_of_the_blood.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_03_diseases_of_the_blood.jpeg

  count_regression_admissions_04_endocrine_nutritional_and_metabolic_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions 04_endocrine_nutritional_and_metabolic poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_04_endocrine_nutritional_and_metabolic.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_04_endocrine_nutritional_and_metabolic.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_04_endocrine_nutritional_and_metabolic.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_04_endocrine_nutritional_and_metabolic.jpeg

  count_regression_admissions_05_mental_and_behavioural_disorders_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions 05_mental_and_behavioural_disorders poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_05_mental_and_behavioural_disorders.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_05_mental_and_behavioural_disorders.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_05_mental_and_behavioural_disorders.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_05_mental_and_behavioural_disorders.jpeg

  count_regression_admissions_06_nervous_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions 06_nervous_system poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_06_nervous_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_06_nervous_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_06_nervous_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_06_nervous_system.jpeg


  count_regression_admissions_09_circulatory_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions 09_circulatory_system poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_09_circulatory_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_09_circulatory_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_09_circulatory_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_09_circulatory_system.jpeg

  count_regression_admissions_10_respiratory_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions 10_respiratory_system poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_10_respiratory_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_10_respiratory_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_10_respiratory_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_10_respiratory_system.jpeg

  count_regression_admissions_11_digestive_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions 11_digestive_system poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_11_digestive_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_11_digestive_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_11_digestive_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_11_digestive_system.jpeg

  count_regression_admissions_12_skin_and_subcutaneous_tissue_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions 12_skin_and_subcutaneous_tissue poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_12_skin_and_subcutaneous_tissue.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_12_skin_and_subcutaneous_tissue.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_12_skin_and_subcutaneous_tissue.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_12_skin_and_subcutaneous_tissue.jpeg

  count_regression_admissions_14_genitourinary_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions 14_genitourinary_system poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_14_genitourinary_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_14_genitourinary_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_14_genitourinary_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_14_genitourinary_system.jpeg

  count_regression_admissions_23_self_harm_and_poisoning_by_drugs_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R admissions 23_self_harm_and_poisoning_by_drugs poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_admissions_23_self_harm_and_poisoning_by_drugs.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_admissions_23_self_harm_and_poisoning_by_drugs.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_admissions_23_self_harm_and_poisoning_by_drugs.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_admissions_23_self_harm_and_poisoning_by_drugs.jpeg

  count_regression_beddays_all_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays all poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_all.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_all.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_all.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_all.jpeg

  count_regression_beddays_01_infectious_and_parasitic_diseases_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays 01_infectious_and_parasitic_diseases poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_01_infectious_and_parasitic_diseases.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_01_infectious_and_parasitic_diseases.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_01_infectious_and_parasitic_diseases.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_01_infectious_and_parasitic_diseases.jpeg

  count_regression_beddays_02_neoplasms_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays 02_neoplasms poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_02_neoplasms.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_02_neoplasms.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_02_neoplasms.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_02_neoplasms.jpeg

  count_regression_beddays_03_diseases_of_the_blood_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays 03_diseases_of_the_blood poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_03_diseases_of_the_blood.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_03_diseases_of_the_blood.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_03_diseases_of_the_blood.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_03_diseases_of_the_blood.jpeg

  count_regression_beddays_04_endocrine_nutritional_and_metabolic_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays 04_endocrine_nutritional_and_metabolic poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_04_endocrine_nutritional_and_metabolic.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_04_endocrine_nutritional_and_metabolic.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_04_endocrine_nutritional_and_metabolic.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_04_endocrine_nutritional_and_metabolic.jpeg

  count_regression_beddays_05_mental_and_behavioural_disorders_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays 05_mental_and_behavioural_disorders poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_05_mental_and_behavioural_disorders.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_05_mental_and_behavioural_disorders.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_05_mental_and_behavioural_disorders.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_05_mental_and_behavioural_disorders.jpeg

  count_regression_beddays_06_nervous_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays 06_nervous_system poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_06_nervous_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_06_nervous_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_06_nervous_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_06_nervous_system.jpeg

  count_regression_beddays_09_circulatory_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays 09_circulatory_system poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_09_circulatory_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_09_circulatory_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_09_circulatory_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_09_circulatory_system.jpeg

  count_regression_beddays_10_respiratory_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays 10_respiratory_system poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_10_respiratory_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_10_respiratory_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_10_respiratory_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_10_respiratory_system.jpeg

  count_regression_beddays_11_digestive_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays 11_digestive_system poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_11_digestive_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_11_digestive_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_11_digestive_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_11_digestive_system.jpeg

  count_regression_beddays_12_skin_and_subcutaneous_tissue_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays 12_skin_and_subcutaneous_tissue poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_12_skin_and_subcutaneous_tissue.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_12_skin_and_subcutaneous_tissue.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_12_skin_and_subcutaneous_tissue.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_12_skin_and_subcutaneous_tissue.jpeg

  count_regression_beddays_14_genitourinary_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays 14_genitourinary_system poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_14_genitourinary_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_14_genitourinary_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_14_genitourinary_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_14_genitourinary_system.jpeg

  count_regression_beddays_23_self_harm_and_poisoning_by_drugs_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R beddays 23_self_harm_and_poisoning_by_drugs poisson uni_var
    needs: [weight_matched_cohort, process_admissions_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_beddays_23_self_harm_and_poisoning_by_drugs.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_beddays_23_self_harm_and_poisoning_by_drugs.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_beddays_23_self_harm_and_poisoning_by_drugs.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_beddays_23_self_harm_and_poisoning_by_drugs.jpeg

  count_regression_outpatient_all_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R outpatient all poisson uni_var
    needs: [weight_matched_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_outpatient_all.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_outpatient_all.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_outpatient_all.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_outpatient_all.jpeg

  count_regression_outpatient_infectious_disease_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R outpatient infectious_disease poisson uni_var
    needs: [weight_matched_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_outpatient_infectious_disease.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_outpatient_infectious_disease.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_outpatient_infectious_disease.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_outpatient_infectious_disease.jpeg

  count_regression_outpatient_oncology_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R outpatient oncology poisson uni_var
    needs: [weight_matched_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_outpatient_oncology.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_outpatient_oncology.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_outpatient_oncology.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_outpatient_oncology.jpeg

  count_regression_outpatient_haematology_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R outpatient haematology poisson uni_var
    needs: [weight_matched_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_outpatient_haematology.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_outpatient_haematology.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_outpatient_haematology.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_outpatient_haematology.jpeg

  count_regression_outpatient_endocrinology_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R outpatient endocrinology poisson uni_var
    needs: [weight_matched_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_outpatient_endocrinology.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_outpatient_endocrinology.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_outpatient_endocrinology.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_outpatient_endocrinology.jpeg

  count_regression_outpatient_mental_health_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R outpatient mental_health poisson uni_var
    needs: [weight_matched_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_outpatient_mental_health.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_outpatient_mental_health.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_outpatient_mental_health.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_outpatient_mental_health.jpeg

  count_regression_outpatient_neurology_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R outpatient neurology poisson uni_var
    needs: [weight_matched_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_outpatient_neurology.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_outpatient_neurology.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_outpatient_neurology.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_outpatient_neurology.jpeg

  count_regression_outpatient_cardiology_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R outpatient cardiology poisson uni_var
    needs: [weight_matched_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_outpatient_cardiology.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_outpatient_cardiology.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_outpatient_cardiology.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_outpatient_cardiology.jpeg

  count_regression_outpatient_respiratory_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R outpatient respiratory poisson uni_var
    needs: [weight_matched_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_outpatient_respiratory.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_outpatient_respiratory.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_outpatient_respiratory.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_outpatient_respiratory.jpeg

  count_regression_outpatient_gastrointestinal_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R outpatient gastrointestinal poisson uni_var
    needs: [weight_matched_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_outpatient_gastrointestinal.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_outpatient_gastrointestinal.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_outpatient_gastrointestinal.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_outpatient_gastrointestinal.jpeg

  count_regression_outpatient_dermatology_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R outpatient dermatology poisson uni_var
    needs: [weight_matched_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_outpatient_dermatology.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_outpatient_dermatology.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_outpatient_dermatology.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_outpatient_dermatology.jpeg

  count_regression_outpatient_renal_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R outpatient renal poisson uni_var
    needs: [weight_matched_cohort, process_outpatient_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_outpatient_renal.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_outpatient_renal.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_outpatient_renal.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_outpatient_renal.jpeg

  count_regression_gp_all_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp all poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_all.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_all.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_all.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_all.jpeg

  count_regression_gp_infectious_disease_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp infectious_disease poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_infectious_disease.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_infectious_disease.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_infectious_disease.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_infectious_disease.jpeg

  count_regression_gp_neoplastic_disease_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp neoplastic_disease poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_neoplastic_disease.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_neoplastic_disease.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_neoplastic_disease.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_neoplastic_disease.jpeg

  count_regression_gp_cellular_component_of_blood_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp cellular_component_of_blood poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_cellular_component_of_blood.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_cellular_component_of_blood.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_cellular_component_of_blood.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_cellular_component_of_blood.jpeg

  count_regression_gp_endocrine_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp endocrine_system poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_endocrine_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_endocrine_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_endocrine_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_endocrine_system.jpeg

  count_regression_gp_mental_disorder_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp mental_disorder poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_mental_disorder.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_mental_disorder.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_mental_disorder.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_mental_disorder.jpeg

  count_regression_gp_nervous_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp nervous_system poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_nervous_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_nervous_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_nervous_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_nervous_system.jpeg

  count_regression_gp_cardiovascular_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp cardiovascular_system poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_cardiovascular_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_cardiovascular_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_cardiovascular_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_cardiovascular_system.jpeg

  count_regression_gp_respiratory_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp respiratory_system poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_respiratory_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_respiratory_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_respiratory_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_respiratory_system.jpeg

  count_regression_gp_digestive_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp digestive_system poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_digestive_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_digestive_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_digestive_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_digestive_system.jpeg

  count_regression_gp_skin_subcutaneous_tissue_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp skin_subcutaneous_tissue poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_skin_subcutaneous_tissue.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_skin_subcutaneous_tissue.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_skin_subcutaneous_tissue.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_skin_subcutaneous_tissue.jpeg

  count_regression_gp_genitourinary_system_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp genitourinary_system poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_genitourinary_system.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_genitourinary_system.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_genitourinary_system.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_genitourinary_system.jpeg

  count_regression_gp_self_harm_poisson_uni_var:
    run: r:latest analysis/08_count_regression.R gp self_harm poisson uni_var
    needs: [weight_matched_cohort, process_gp_data]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/uni_var/tables/crude_rates_gp_self_harm.csv
        model_coefficients: output/descriptives/matched_cohort/poisson/uni_var/tables/coeff_gp_self_harm.csv
        model_stats: output/descriptives/matched_cohort/poisson/uni_var/tables/stats_gp_self_harm.csv
        rr_plot: output/descriptives/matched_cohort/poisson/uni_var/plots/rrplot_gp_self_harm.jpeg

  summarise_irr:
    run: r:latest analysis/08_summarise_irr.R poisson uni_var
    needs: [count_regression_admissions_all_poisson_uni_var,
            count_regression_admissions_01_infectious_and_parasitic_diseases_poisson_uni_var,
            count_regression_admissions_02_neoplasms_poisson_uni_var,
            count_regression_admissions_03_diseases_of_the_blood_poisson_uni_var,
            count_regression_admissions_04_endocrine_nutritional_and_metabolic_poisson_uni_var,
            count_regression_admissions_05_mental_and_behavioural_disorders_poisson_uni_var,
            count_regression_admissions_06_nervous_system_poisson_uni_var,
            count_regression_admissions_09_circulatory_system_poisson_uni_var,
            count_regression_admissions_10_respiratory_system_poisson_uni_var,
            count_regression_admissions_11_digestive_system_poisson_uni_var,
            count_regression_admissions_12_skin_and_subcutaneous_tissue_poisson_uni_var,
            count_regression_admissions_14_genitourinary_system_poisson_uni_var,
            count_regression_admissions_23_self_harm_and_poisoning_by_drugs_poisson_uni_var,
            count_regression_beddays_all_poisson_uni_var,
            count_regression_beddays_01_infectious_and_parasitic_diseases_poisson_uni_var,
            count_regression_beddays_02_neoplasms_poisson_uni_var,
            count_regression_beddays_03_diseases_of_the_blood_poisson_uni_var,
            count_regression_beddays_04_endocrine_nutritional_and_metabolic_poisson_uni_var,
            count_regression_beddays_05_mental_and_behavioural_disorders_poisson_uni_var,
            count_regression_beddays_06_nervous_system_poisson_uni_var,
            count_regression_beddays_09_circulatory_system_poisson_uni_var,
            count_regression_beddays_10_respiratory_system_poisson_uni_var,
            count_regression_beddays_11_digestive_system_poisson_uni_var,
            count_regression_beddays_12_skin_and_subcutaneous_tissue_poisson_uni_var,
            count_regression_beddays_14_genitourinary_system_poisson_uni_var,
            count_regression_beddays_23_self_harm_and_poisoning_by_drugs_poisson_uni_var,
            count_regression_outpatient_all_poisson_uni_var,
            count_regression_outpatient_infectious_disease_poisson_uni_var,
            count_regression_outpatient_oncology_poisson_uni_var,
            count_regression_outpatient_haematology_poisson_uni_var,
            count_regression_outpatient_endocrinology_poisson_uni_var,
            count_regression_outpatient_mental_health_poisson_uni_var,
            count_regression_outpatient_neurology_poisson_uni_var,
            count_regression_outpatient_cardiology_poisson_uni_var,
            count_regression_outpatient_respiratory_poisson_uni_var,
            count_regression_outpatient_gastrointestinal_poisson_uni_var,
            count_regression_outpatient_dermatology_poisson_uni_var,
            count_regression_outpatient_renal_poisson_uni_var,
            count_regression_gp_all_poisson_uni_var,
            count_regression_gp_infectious_disease_poisson_uni_var,
            count_regression_gp_neoplastic_disease_poisson_uni_var,
            count_regression_gp_cellular_component_of_blood_poisson_uni_var,
            count_regression_gp_endocrine_system_poisson_uni_var,
            count_regression_gp_mental_disorder_poisson_uni_var,
            count_regression_gp_nervous_system_poisson_uni_var,
            count_regression_gp_cardiovascular_system_poisson_uni_var,
            count_regression_gp_respiratory_system_poisson_uni_var,
            count_regression_gp_digestive_system_poisson_uni_var,
            count_regression_gp_skin_subcutaneous_tissue_poisson_uni_var,
            count_regression_gp_genitourinary_system_poisson_uni_var,
            count_regression_gp_self_harm_poisson_uni_var]
    outputs:
      moderately_sensitive:
        crude_rates: output/descriptives/matched_cohort/poisson/summarised_uni_var/crude_rates.csv
        irr_table: output/descriptives/matched_cohort/poisson/summarised_uni_var/table_irr.csv
        irr_plot_positive: output/descriptives/matched_cohort/poisson/summarised_uni_var/plot_irr_positive.jpeg
        irr_plot_all: output/descriptives/matched_cohort/poisson/summarised_uni_var/plot_irr_all.jpeg

  generate_positive_cohort:
    run: r:latest analysis/09_construct_positive_cohort.R
    needs: [process_patient_data, process_admissions_data, process_outpatient_data, process_gp_data]
    outputs:
      moderately_sensitive:
        cohort_flowchart: output/descriptives/positive_cohort/tbl_flowchart.csv
      highly_sensitive:
        resource_data: output/data/data_resource.rds
        patient_data: output/data/data_positives.rds

  summarise_positive_cohort:
    run: r:latest analysis/09_summarise_positive_cohort.R
    needs: [generate_positive_cohort]
    outputs:
      moderately_sensitive:
        tbl_cohort_summary: output/descriptives/positive_cohort/tbl_cohort_summary.csv
        tbl_daily_beddays: output/descriptives/positive_cohort/tbl_daily_beddays.csv
        tbl_daily_critical_care: output/descriptives/positive_cohort/tbl_daily_critical_care.csv
        tbl_daily_outpatient: output/descriptives/positive_cohort/tbl_daily_outpatient.csv
        tbl_daily_gp: output/descriptives/positive_cohort/tbl_daily_gp.csv
        plot_daily_beddays: output/descriptives/positive_cohort/plot_daily_beddays.jpeg
        plot_daily_critical_care: output/descriptives/positive_cohort/plot_daily_critical_care.jpeg
        plot_daily_outpatient: output/descriptives/positive_cohort/plot_daily_outpatient.jpeg
        plot_daily_gp: output/descriptives/positive_cohort/plot_daily_gp.jpeg


  mcc_data_prep:
    run: r:latest analysis/10_1_MCC_prep_resource.R
    needs: [generate_positive_cohort]
    outputs:
      highly_sensitive:
        mcc_resource_data: output/data/data_resource_mcc.rds

  mcc_run_model_and_selection:
    run: r:latest analysis/10_2_MCC_model_selection.R 5
    needs: [mcc_data_prep]
    outputs:
      highly_sensitive:
        model_data_1: output/mcc/model/MCC_H1_M150.RData
        model_data_2: output/mcc/model/MCC_H2_M150.RData
        model_data_3: output/mcc/model/MCC_H3_M150.RData
        model_data_4: output/mcc/model/MCC_H4_M150.RData
        model_data_5: output/mcc/model/MCC_H5_M150.RData
        approxMCL: output/mcc/model/MCCModSelCrits_approxMCL.RData
        approxML: output/mcc/model/MCCModSelCrits_approxML.RData
        postMode: output/mcc/model/MCCModSelCrits_postMode.RData
      moderately_sensitive:
        tbl_model_selection: output/mcc/model/model_selection_criteria.csv

  mcc_results:
    run: r:latest analysis/10_3_MCC_class_allocations_visualization.R
    needs: [mcc_run_model_and_selection]
    outputs:
      highly_sensitive:
        allocations: output/mcc/allocations/allocations.csv
      moderately_sensitive:
        heatmap: output/mcc/plots/heatmap.jpeg

  dtw_data_prep:
    run: r:latest analysis/11_1_DTW_prep_resource.R
    needs: [generate_positive_cohort]
    outputs:
      highly_sensitive:
        dtw_timeseries_data: output/data/data_timeseries_dtw.rds
        dtw_resource_data: output/data/data_resource_dtw.rds
        dtw_patient_data: output/data/data_positives_dtw.rds

  dtw_run_model_4:
    run: r:latest analysis/11_2_DTW_tsclust.R 4
    needs: [dtw_data_prep]
    outputs:
      highly_sensitive:
        ts_cluster: output/dtw/tsclust/tsclust_4.rds
        cv_indicies: output/dtw/cv_indicies/tbl_cv_indicies_4.csv
        cluster: output/dtw/data_cluster/data_cluster_4.rds

  dtw_run_model_5:
    run: r:latest analysis/11_2_DTW_tsclust.R 5
    needs: [dtw_data_prep]
    outputs:
      highly_sensitive:
        ts_cluster: output/dtw/tsclust/tsclust_5.rds
        cv_indicies: output/dtw/cv_indicies/tbl_cv_indicies_5.csv
        cluster: output/dtw/data_cluster/data_cluster_5.rds

  dtw_run_model_6:
    run: r:latest analysis/11_2_DTW_tsclust.R 6
    needs: [dtw_data_prep]
    outputs:
      highly_sensitive:
        ts_cluster: output/dtw/tsclust/tsclust_6.rds
        cv_indicies: output/dtw/cv_indicies/tbl_cv_indicies_6.csv
        cluster: output/dtw/data_cluster/data_cluster_6.rds

  dtw_run_model_7:
    run: r:latest analysis/11_2_DTW_tsclust.R 7
    needs: [dtw_data_prep]
    outputs:
      highly_sensitive:
        ts_cluster: output/dtw/tsclust/tsclust_7.rds
        cv_indicies: output/dtw/cv_indicies/tbl_cv_indicies_7.csv
        cluster: output/dtw/data_cluster/data_cluster_7.rds

  dtw_run_model_8:
    run: r:latest analysis/11_2_DTW_tsclust.R 8
    needs: [dtw_data_prep]
    outputs:
      highly_sensitive:
        ts_cluster: output/dtw/tsclust/tsclust_8.rds
        cv_indicies: output/dtw/cv_indicies/tbl_cv_indicies_8.csv
        cluster: output/dtw/data_cluster/data_cluster_8.rds

  dtw_selection:
    run: r:latest analysis/11_3_DTW_selection.R
    needs: [dtw_run_model_4, dtw_run_model_5, dtw_run_model_6, dtw_run_model_7, dtw_run_model_8]
    outputs:
      moderately_sensitive:
        tbl_cvi: output/dtw/selection/tbl_cluster_validity.csv
        plot_cvi: output/dtw/selection/plot_cluster_validity.jpeg

  dtw_results_4:
    run: r:latest analysis/11_4_DTW_results.R 4
    needs: [dtw_data_prep, dtw_run_model_4]
    outputs:
      moderately_sensitive:
        tbl_summary: output/dtw/results/tbl_summary_4.csv
        tbl_resource_use: output/dtw/results/tbl_resource_use_cluster_4.csv
        plot_resource_use: output/dtw/results/plot_resource_use_cluster_4.jpeg
        tbl_multinom_coef: output/dtw/results/tbl_multinom_coef_4.csv
        tbl_multinom_metrics: output/dtw/results/tbl_multinom_metrics_4.csv
        plot_multinom_coef: output/dtw/results/plot_multinom_coef_4.jpeg

  dtw_results_5:
    run: r:latest analysis/11_4_DTW_results.R 5
    needs: [dtw_data_prep, dtw_run_model_5]
    outputs:
      moderately_sensitive:
        tbl_summary: output/dtw/results/tbl_summary_5.csv
        tbl_resource_use: output/dtw/results/tbl_resource_use_cluster_5.csv
        plot_resource_use: output/dtw/results/plot_resource_use_cluster_5.jpeg
        tbl_multinom_coef: output/dtw/results/tbl_multinom_coef_5.csv
        tbl_multinom_metrics: output/dtw/results/tbl_multinom_metrics_5.csv
        plot_multinom_coef: output/dtw/results/plot_multinom_coef_5.jpeg

  dtw_results_6:
    run: r:latest analysis/11_4_DTW_results.R 6
    needs: [dtw_data_prep, dtw_run_model_6]
    outputs:
      moderately_sensitive:
        tbl_summary: output/dtw/results/tbl_summary_6.csv
        tbl_resource_use: output/dtw/results/tbl_resource_use_cluster_6.csv
        plot_resource_use: output/dtw/results/plot_resource_use_cluster_6.jpeg
        tbl_multinom_coef: output/dtw/results/tbl_multinom_coef_6.csv
        tbl_multinom_metrics: output/dtw/results/tbl_multinom_metrics_6.csv
        plot_multinom_coef: output/dtw/results/plot_multinom_coef_6.jpeg

  dtw_results_7:
    run: r:latest analysis/11_4_DTW_results.R 7
    needs: [dtw_data_prep, dtw_run_model_7]
    outputs:
      moderately_sensitive:
        tbl_summary: output/dtw/results/tbl_summary_7.csv
        tbl_resource_use: output/dtw/results/tbl_resource_use_cluster_7.csv
        plot_resource_use: output/dtw/results/plot_resource_use_cluster_7.jpeg
        tbl_multinom_coef: output/dtw/results/tbl_multinom_coef_7.csv
        tbl_multinom_metrics: output/dtw/results/tbl_multinom_metrics_7.csv
        plot_multinom_coef: output/dtw/results/plot_multinom_coef_7.jpeg

  dtw_results_8:
    run: r:latest analysis/11_4_DTW_results.R 8
    needs: [dtw_data_prep, dtw_run_model_8]
    outputs:
      moderately_sensitive:
        tbl_summary: output/dtw/results/tbl_summary_8.csv
        tbl_resource_use: output/dtw/results/tbl_resource_use_cluster_8.csv
        plot_resource_use: output/dtw/results/plot_resource_use_cluster_8.jpeg
        tbl_multinom_coef: output/dtw/results/tbl_multinom_coef_8.csv
        tbl_multinom_metrics: output/dtw/results/tbl_multinom_metrics_8.csv
        plot_multinom_coef: output/dtw/results/plot_multinom_coef_8.jpeg

  lcmm_data_prep:
    run: r:latest analysis/12_1_LCMM_data_prep.R
    needs: [generate_positive_cohort]
    outputs:
      highly_sensitive:
        lcmm_resource_data: output/data/data_resource_lcmm.rds
        lcmm_patient_data: output/data/data_positives_lcmm.rds
      moderately_sensitive:
        lcmm_resource_summary: output/lcmm/summary_data_resource_lcmm.csv

  lcmm_link_function_beddays:
    run: r:latest analysis/12_2_LCMM_link_function.R beddays
    needs: [lcmm_data_prep]
    outputs:
      moderately_sensitive:
        table_model_fits: output/lcmm/beddays/link_function/tbl_link_model_fit.csv
        table_estimlink: output/lcmm/beddays/link_function/tbl_estimlink.csv
        plot_estimlink: output/lcmm/beddays/link_function/plot_estimlink.jpeg

  lcmm_link_function_outpatient:
    run: r:latest analysis/12_2_LCMM_link_function.R outpatient
    needs: [lcmm_data_prep]
    outputs:
      moderately_sensitive:
        table_model_fits: output/lcmm/outpatient/link_function/tbl_link_model_fit.csv
        table_estimlink: output/lcmm/outpatient/link_function/tbl_estimlink.csv
        plot_estimlink: output/lcmm/outpatient/link_function/plot_estimlink.jpeg

  lcmm_link_function_gp:
    run: r:latest analysis/12_2_LCMM_link_function.R gp
    needs: [lcmm_data_prep]
    outputs:
      moderately_sensitive:
        table_model_fits: output/lcmm/gp/link_function/tbl_link_model_fit.csv
        table_estimlink: output/lcmm/gp/link_function/tbl_estimlink.csv
        plot_estimlink: output/lcmm/gp/link_function/plot_estimlink.jpeg

  lcmm_run_model_1_beddays:
    run: r:latest analysis/12_2_LCMM_model.R 1 beddays
    needs: [lcmm_data_prep]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/beddays/models/lcmm_model_1.rds

  lcmm_run_model_2_beddays:
    run: r:latest analysis/12_2_LCMM_model.R 2 beddays
    needs: [lcmm_data_prep, lcmm_run_model_1_beddays]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/beddays/models/lcmm_model_2.rds

  lcmm_run_model_3_beddays:
    run: r:latest analysis/12_2_LCMM_model.R 3 beddays
    needs: [lcmm_data_prep, lcmm_run_model_1_beddays]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/beddays/models/lcmm_model_3.rds

  lcmm_run_model_4_beddays:
    run: r:latest analysis/12_2_LCMM_model.R 4 beddays
    needs: [lcmm_data_prep, lcmm_run_model_1_beddays]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/beddays/models/lcmm_model_4.rds

  lcmm_run_model_5_beddays:
    run: r:latest analysis/12_2_LCMM_model.R 5 beddays
    needs: [lcmm_data_prep, lcmm_run_model_1_beddays]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/beddays/models/lcmm_model_5.rds

  lcmm_model_selection_beddays:
    run: r:latest analysis/12_3_LCMM_selection.R beddays
    needs: [lcmm_data_prep, lcmm_run_model_1_beddays, lcmm_run_model_2_beddays, lcmm_run_model_3_beddays,
            lcmm_run_model_4_beddays, lcmm_run_model_5_beddays]
    outputs:
      moderately_sensitive:
        table_model_metrics: output/lcmm/beddays/selection/tbl_model_metrics.csv
        table_class_probability: output/lcmm/beddays/selection/tbl_class_probability.csv
        table_class_proportion: output/lcmm/beddays/selection/tbl_class_proportion.csv
        plot_BIC: output/lcmm/beddays/selection/plot_BIC.jpeg
        plot_loglik: output/lcmm/beddays/selection/plot_loglik.jpeg
        plot_class_probability: output/lcmm/beddays/selection/plot_class_probability.jpeg
        plot_class_proportion: output/lcmm/beddays/selection/plot_class_proportion.jpeg 

  lcmm_results_1_beddays:
    run: r:latest analysis/12_4_LCMM_results.R 1 beddays
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_1_beddays]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/beddays/summary_tbl/tbl_summary_1.csv
        table_observed_trajectory: output/lcmm/beddays/obs_trajectory/tbl_obs_trajectory_1.csv
        plot_observed_trajectory: output/lcmm/beddays/obs_trajectory/plot_observed_trajectory_1.jpeg
        table_predicted_trajectory: output/lcmm/beddays/pred_trajectory/tbl_predicted_trajectory_1.csv
        plot_predicted_trajectory: output/lcmm/beddays/pred_trajectory/plot_predicted_trajectory_1.jpeg
        model_summary: output/lcmm/beddays/model_summary/model_summary_1.txt
        tbl_multinom_coef: output/lcmm/beddays/multinomial/tbl_multinom_coef_1.csv
        tbl_multinom_metrics: output/lcmm/beddays/multinomial/tbl_multinom_metrics_1.csv
        plot_multinom_coef: output/lcmm/beddays/multinomial/plot_multinom_coef_1.jpeg

  lcmm_results_2_beddays:
    run: r:latest analysis/12_4_LCMM_results.R 2 beddays
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_2_beddays]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/beddays/summary_tbl/tbl_summary_2.csv
        table_observed_trajectory: output/lcmm/beddays/obs_trajectory/tbl_obs_trajectory_2.csv
        plot_observed_trajectory: output/lcmm/beddays/obs_trajectory/plot_observed_trajectory_2.jpeg
        table_predicted_trajectory: output/lcmm/beddays/pred_trajectory/tbl_predicted_trajectory_2.csv
        plot_predicted_trajectory: output/lcmm/beddays/pred_trajectory/plot_predicted_trajectory_2.jpeg
        model_summary: output/lcmm/beddays/model_summary/model_summary_2.txt
        tbl_multinom_coef: output/lcmm/beddays/multinomial/tbl_multinom_coef_2.csv
        tbl_multinom_metrics: output/lcmm/beddays/multinomial/tbl_multinom_metrics_2.csv
        plot_multinom_coef: output/lcmm/beddays/multinomial/plot_multinom_coef_2.jpeg

  lcmm_results_3_beddays:
    run: r:latest analysis/12_4_LCMM_results.R 3 beddays
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_3_beddays]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/beddays/summary_tbl/tbl_summary_3.csv
        table_observed_trajectory: output/lcmm/beddays/obs_trajectory/tbl_obs_trajectory_3.csv
        plot_observed_trajectory: output/lcmm/beddays/obs_trajectory/plot_observed_trajectory_3.jpeg
        table_predicted_trajectory: output/lcmm/beddays/pred_trajectory/tbl_predicted_trajectory_3.csv
        plot_predicted_trajectory: output/lcmm/beddays/pred_trajectory/plot_predicted_trajectory_3.jpeg
        model_summary: output/lcmm/beddays/model_summary/model_summary_3.txt
        tbl_multinom_coef: output/lcmm/beddays/multinomial/tbl_multinom_coef_3.csv
        tbl_multinom_metrics: output/lcmm/beddays/multinomial/tbl_multinom_metrics_3.csv
        plot_multinom_coef: output/lcmm/beddays/multinomial/plot_multinom_coef_3.jpeg

  lcmm_results_4_beddays:
    run: r:latest analysis/12_4_LCMM_results.R 4 beddays
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_4_beddays]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/beddays/summary_tbl/tbl_summary_4.csv
        table_observed_trajectory: output/lcmm/beddays/obs_trajectory/tbl_obs_trajectory_4.csv
        plot_observed_trajectory: output/lcmm/beddays/obs_trajectory/plot_observed_trajectory_4.jpeg
        table_predicted_trajectory: output/lcmm/beddays/pred_trajectory/tbl_predicted_trajectory_4.csv
        plot_predicted_trajectory: output/lcmm/beddays/pred_trajectory/plot_predicted_trajectory_4.jpeg
        model_summary: output/lcmm/beddays/model_summary/model_summary_4.txt
        tbl_multinom_coef: output/lcmm/beddays/multinomial/tbl_multinom_coef_4.csv
        tbl_multinom_metrics: output/lcmm/beddays/multinomial/tbl_multinom_metrics_4.csv
        plot_multinom_coef: output/lcmm/beddays/multinomial/plot_multinom_coef_4.jpeg

  lcmm_results_5_beddays:
    run: r:latest analysis/12_4_LCMM_results.R 5 beddays
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_5_beddays]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/beddays/summary_tbl/tbl_summary_5.csv
        table_observed_trajectory: output/lcmm/beddays/obs_trajectory/tbl_obs_trajectory_5.csv
        plot_observed_trajectory: output/lcmm/beddays/obs_trajectory/plot_observed_trajectory_5.jpeg
        table_predicted_trajectory: output/lcmm/beddays/pred_trajectory/tbl_predicted_trajectory_5.csv
        plot_predicted_trajectory: output/lcmm/beddays/pred_trajectory/plot_predicted_trajectory_5.jpeg
        model_summary: output/lcmm/beddays/model_summary/model_summary_5.txt
        tbl_multinom_coef: output/lcmm/beddays/multinomial/tbl_multinom_coef_5.csv
        tbl_multinom_metrics: output/lcmm/beddays/multinomial/tbl_multinom_metrics_5.csv
        plot_multinom_coef: output/lcmm/beddays/multinomial/plot_multinom_coef_5.jpeg

  lcmm_run_model_1_outpatient:
    run: r:latest analysis/12_2_LCMM_model.R 1 outpatient
    needs: [lcmm_data_prep]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/outpatient/models/lcmm_model_1.rds

  lcmm_run_model_2_outpatient:
    run: r:latest analysis/12_2_LCMM_model.R 2 outpatient
    needs: [lcmm_data_prep, lcmm_run_model_1_outpatient]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/outpatient/models/lcmm_model_2.rds

  lcmm_run_model_3_outpatient:
    run: r:latest analysis/12_2_LCMM_model.R 3 outpatient
    needs: [lcmm_data_prep, lcmm_run_model_1_outpatient]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/outpatient/models/lcmm_model_3.rds

  lcmm_run_model_4_outpatient:
    run: r:latest analysis/12_2_LCMM_model.R 4 outpatient
    needs: [lcmm_data_prep, lcmm_run_model_1_outpatient]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/outpatient/models/lcmm_model_4.rds

  lcmm_run_model_5_outpatient:
    run: r:latest analysis/12_2_LCMM_model.R 5 outpatient
    needs: [lcmm_data_prep, lcmm_run_model_1_outpatient]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/outpatient/models/lcmm_model_5.rds

  lcmm_model_selection_outpatient:
    run: r:latest analysis/12_3_LCMM_selection.R outpatient
    needs: [lcmm_data_prep, lcmm_run_model_1_outpatient, lcmm_run_model_2_outpatient, lcmm_run_model_3_outpatient,
            lcmm_run_model_4_outpatient, lcmm_run_model_5_outpatient]
    outputs:
      moderately_sensitive:
        table_model_metrics: output/lcmm/outpatient/selection/tbl_model_metrics.csv
        table_class_probability: output/lcmm/outpatient/selection/tbl_class_probability.csv
        table_class_proportion: output/lcmm/outpatient/selection/tbl_class_proportion.csv
        plot_AIC: output/lcmm/outpatient/selection/plot_AIC.jpeg
        plot_BIC: output/lcmm/outpatient/selection/plot_BIC.jpeg
        plot_loglik: output/lcmm/outpatient/selection/plot_loglik.jpeg
        plot_class_probability: output/lcmm/outpatient/selection/plot_class_probability.jpeg
        plot_class_proportion: output/lcmm/outpatient/selection/plot_class_proportion.jpeg 

  lcmm_results_1_outpatient:
    run: r:latest analysis/12_4_LCMM_results.R 1 outpatient
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_1_outpatient]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/outpatient/summary_tbl/tbl_summary_1.csv
        table_observed_trajectory: output/lcmm/outpatient/obs_trajectory/tbl_obs_trajectory_1.csv
        plot_observed_trajectory: output/lcmm/outpatient/obs_trajectory/plot_observed_trajectory_1.jpeg
        table_predicted_trajectory: output/lcmm/outpatient/pred_trajectory/tbl_predicted_trajectory_1.csv
        plot_predicted_trajectory: output/lcmm/outpatient/pred_trajectory/plot_predicted_trajectory_1.jpeg
        model_summary: output/lcmm/outpatient/model_summary/model_summary_1.txt

  lcmm_results_2_outpatient:
    run: r:latest analysis/12_4_LCMM_results.R 2 outpatient
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_2_outpatient]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/outpatient/summary_tbl/tbl_summary_2.csv
        table_observed_trajectory: output/lcmm/outpatient/obs_trajectory/tbl_obs_trajectory_2.csv
        plot_observed_trajectory: output/lcmm/outpatient/obs_trajectory/plot_observed_trajectory_2.jpeg
        table_predicted_trajectory: output/lcmm/outpatient/pred_trajectory/tbl_predicted_trajectory_2.csv
        plot_predicted_trajectory: output/lcmm/outpatient/pred_trajectory/plot_predicted_trajectory_2.jpeg
        model_summary: output/lcmm/outpatient/model_summary/model_summary_2.txt

  lcmm_results_3_outpatient:
    run: r:latest analysis/12_4_LCMM_results.R 3 outpatient
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_3_outpatient]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/outpatient/summary_tbl/tbl_summary_3.csv
        table_observed_trajectory: output/lcmm/outpatient/obs_trajectory/tbl_obs_trajectory_3.csv
        plot_observed_trajectory: output/lcmm/outpatient/obs_trajectory/plot_observed_trajectory_3.jpeg
        table_predicted_trajectory: output/lcmm/outpatient/pred_trajectory/tbl_predicted_trajectory_3.csv
        plot_predicted_trajectory: output/lcmm/outpatient/pred_trajectory/plot_predicted_trajectory_3.jpeg
        model_summary: output/lcmm/outpatient/model_summary/model_summary_3.txt

  lcmm_results_4_outpatient:
    run: r:latest analysis/12_4_LCMM_results.R 4 outpatient
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_4_outpatient]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/outpatient/summary_tbl/tbl_summary_4.csv
        table_observed_trajectory: output/lcmm/outpatient/obs_trajectory/tbl_obs_trajectory_4.csv
        plot_observed_trajectory: output/lcmm/outpatient/obs_trajectory/plot_observed_trajectory_4.jpeg
        table_predicted_trajectory: output/lcmm/outpatient/pred_trajectory/tbl_predicted_trajectory_4.csv
        plot_predicted_trajectory: output/lcmm/outpatient/pred_trajectory/plot_predicted_trajectory_4.jpeg
        model_summary: output/lcmm/outpatient/model_summary/model_summary_4.txt

  lcmm_results_5_outpatient:
    run: r:latest analysis/12_4_LCMM_results.R 5 outpatient
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_5_outpatient]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/outpatient/summary_tbl/tbl_summary_5.csv
        table_observed_trajectory: output/lcmm/outpatient/obs_trajectory/tbl_obs_trajectory_5.csv
        plot_observed_trajectory: output/lcmm/outpatient/obs_trajectory/plot_observed_trajectory_5.jpeg
        table_predicted_trajectory: output/lcmm/outpatient/pred_trajectory/tbl_predicted_trajectory_5.csv
        plot_predicted_trajectory: output/lcmm/outpatient/pred_trajectory/plot_predicted_trajectory_5.jpeg
        model_summary: output/lcmm/outpatient/model_summary/model_summary_5.txt

  lcmm_run_model_1_gp:
    run: r:latest analysis/12_2_LCMM_model.R 1 gp
    needs: [lcmm_data_prep]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/gp/models/lcmm_model_1.rds

  lcmm_run_model_2_gp:
    run: r:latest analysis/12_2_LCMM_model.R 2 gp
    needs: [lcmm_data_prep, lcmm_run_model_1_gp]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/gp/models/lcmm_model_2.rds

  lcmm_run_model_3_gp:
    run: r:latest analysis/12_2_LCMM_model.R 3 gp
    needs: [lcmm_data_prep, lcmm_run_model_1_gp]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/gp/models/lcmm_model_3.rds

  lcmm_run_model_4_gp:
    run: r:latest analysis/12_2_LCMM_model.R 4 gp
    needs: [lcmm_data_prep, lcmm_run_model_1_gp]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/gp/models/lcmm_model_4.rds

  lcmm_run_model_5_gp:
    run: r:latest analysis/12_2_LCMM_model.R 5 gp
    needs: [lcmm_data_prep, lcmm_run_model_1_gp]
    outputs:
      highly_sensitive:
        lcmm_model: output/lcmm/gp/models/lcmm_model_5.rds

  lcmm_model_selection_gp:
    run: r:latest analysis/12_3_LCMM_selection.R gp
    needs: [lcmm_data_prep, lcmm_run_model_1_gp, lcmm_run_model_2_gp, lcmm_run_model_3_gp,
            lcmm_run_model_4_gp, lcmm_run_model_5_gp]
    outputs:
      moderately_sensitive:
        table_model_metrics: output/lcmm/gp/selection/tbl_model_metrics.csv
        table_class_probability: output/lcmm/gp/selection/tbl_class_probability.csv
        table_class_proportion: output/lcmm/gp/selection/tbl_class_proportion.csv
        plot_BIC: output/lcmm/gp/selection/plot_BIC.jpeg
        plot_loglik: output/lcmm/gp/selection/plot_loglik.jpeg
        plot_class_probability: output/lcmm/gp/selection/plot_class_probability.jpeg
        plot_class_proportion: output/lcmm/gp/selection/plot_class_proportion.jpeg 

  lcmm_results_1_gp:
    run: r:latest analysis/12_4_LCMM_results.R 1 gp
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_1_gp]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/gp/summary_tbl/tbl_summary_1.csv
        table_observed_trajectory: output/lcmm/gp/obs_trajectory/tbl_obs_trajectory_1.csv
        plot_observed_trajectory: output/lcmm/gp/obs_trajectory/plot_observed_trajectory_1.jpeg
        table_predicted_trajectory: output/lcmm/gp/pred_trajectory/tbl_predicted_trajectory_1.csv
        plot_predicted_trajectory: output/lcmm/gp/pred_trajectory/plot_predicted_trajectory_1.jpeg
        model_summary: output/lcmm/gp/model_summary/model_summary_1.txt

  lcmm_results_2_gp:
    run: r:latest analysis/12_4_LCMM_results.R 2 gp
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_2_gp]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/gp/summary_tbl/tbl_summary_2.csv
        table_observed_trajectory: output/lcmm/gp/obs_trajectory/tbl_obs_trajectory_2.csv
        plot_observed_trajectory: output/lcmm/gp/obs_trajectory/plot_observed_trajectory_2.jpeg
        table_predicted_trajectory: output/lcmm/gp/pred_trajectory/tbl_predicted_trajectory_2.csv
        plot_predicted_trajectory: output/lcmm/gp/pred_trajectory/plot_predicted_trajectory_2.jpeg
        model_summary: output/lcmm/gp/model_summary/model_summary_2.txt

  lcmm_results_3_gp:
    run: r:latest analysis/12_4_LCMM_results.R 3 gp
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_3_gp]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/gp/summary_tbl/tbl_summary_3.csv
        table_observed_trajectory: output/lcmm/gp/obs_trajectory/tbl_obs_trajectory_3.csv
        plot_observed_trajectory: output/lcmm/gp/obs_trajectory/plot_observed_trajectory_3.jpeg
        table_predicted_trajectory: output/lcmm/gp/pred_trajectory/tbl_predicted_trajectory_3.csv
        plot_predicted_trajectory: output/lcmm/gp/pred_trajectory/plot_predicted_trajectory_3.jpeg
        model_summary: output/lcmm/gp/model_summary/model_summary_3.txt

  lcmm_results_4_gp:
    run: r:latest analysis/12_4_LCMM_results.R 4 gp
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_4_gp]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/gp/summary_tbl/tbl_summary_4.csv
        table_observed_trajectory: output/lcmm/gp/obs_trajectory/tbl_obs_trajectory_4.csv
        plot_observed_trajectory: output/lcmm/gp/obs_trajectory/plot_observed_trajectory_4.jpeg
        table_predicted_trajectory: output/lcmm/gp/pred_trajectory/tbl_predicted_trajectory_4.csv
        plot_predicted_trajectory: output/lcmm/gp/pred_trajectory/plot_predicted_trajectory_4.jpeg
        model_summary: output/lcmm/gp/model_summary/model_summary_4.txt

  lcmm_results_5_gp:
    run: r:latest analysis/12_4_LCMM_results.R 5 gp
    needs: [generate_positive_cohort, lcmm_data_prep, lcmm_run_model_5_gp]
    outputs:
      moderately_sensitive:
        table_summary: output/lcmm/gp/summary_tbl/tbl_summary_5.csv
        table_observed_trajectory: output/lcmm/gp/obs_trajectory/tbl_obs_trajectory_5.csv
        plot_observed_trajectory: output/lcmm/gp/obs_trajectory/plot_observed_trajectory_5.jpeg
        table_predicted_trajectory: output/lcmm/gp/pred_trajectory/tbl_predicted_trajectory_5.csv
        plot_predicted_trajectory: output/lcmm/gp/pred_trajectory/plot_predicted_trajectory_5.jpeg
        model_summary: output/lcmm/gp/model_summary/model_summary_5.txt