_pkgdown.yml

url: https://ohdsi.github.io/CohortGenerator/

template:
  bootstrap: 5
  bslib:
    bootswatch: cosmo

home:
  links:
  - text: Ask a question
    href: http://forums.ohdsi.org

reference:
  - title: "Cohort Generation"
    desc: >
      Functions that support generating cohorts.
    contents:
      - runCohortGeneration
      - generateCohortSet

  - title: "Cohort Tables"
    desc: >
      Functions that support creating the necessary cohort tables.
    contents:
      - createCohortTables
      - getCohortTableNames

  - title: "Cohort Defintion Set"
    desc: >
      Functions that support working with a cohort definition set
    contents:
      - saveCohortDefinitionSet
      - getCohortDefinitionSet
      - createEmptyCohortDefinitionSet
      - checkAndFixCohortDefinitionSetDataTypes
      - isCohortDefinitionSet
      
  - title: "Cohort Counts"
    desc: >
      Function for obtaining the counts of subjects and events for one or
      more cohorts
    contents:
      - getCohortCounts
      
  - title: "Cohort Subset Functions"
    desc: >
      Functions for creating cohort subset definitions and subset operators.
    contents:
      - addCohortSubsetDefinition
      - createCohortSubset
      - createCohortSubsetDefinition
      - createDemographicSubset
      - createLimitSubset
      - createSubsetCohortWindow
      - getSubsetDefinitions
      - saveCohortSubsetDefinition

  - title: "Cohort Subset Classes"
    desc: >
      R6 classes for cohort subset definitions and subset operators.
    contents:
      - CohortSubsetDefinition
      - CohortSubsetOperator
      - DemographicSubsetOperator
      - LimitSubsetOperator
      - SubsetCohortWindow
      - SubsetOperator
      
  - title: "Cohort Statistics"
    desc: >
      Functions for inserting inclusion rule names from a cohort definition,
      exporting the cohort statistics to the file system and a helper function 
      for dropping those tables when they are no longer needed. These functions
      assume you are using [Circe](https://github.com/OHDSI/circe-be) for 
      inclusion rules and cohort statistics.
    contents:
      - getCohortStats
      - getCohortInclusionRules
      - insertInclusionRuleNames
      - exportCohortStatsTables
      - dropCohortStatsTables
      
  - title: "Negative Control Outcomes"
    desc: >
      Functions for creating negative control outcome cohorts for use in
      population-level estimation.
    contents:
      - createEmptyNegativeControlOutcomeCohortSet
      - generateNegativeControlOutcomeCohorts
      
  - title: "Result Model Management"
    desc: >
      Functions for managing the results of running Cohort Generator via
      `runCohortGeneration`
    contents:
      - createResultsDataModel
      - getDataMigrator
      - getResultsDataModelSpecifications
      - migrateDataModel
      - uploadResults

  - title: "CSV File Helpers"
    desc: >
      Functions for reading and writing CSV files to ensure adherance to
      the HADES standard when interfacing between R and SQL/File System:
      https://ohdsi.github.io/Hades/codeStyle.html#Interfacing_between_R_and_SQL
    contents:
      - readCsv
      - writeCsv
      - isCamelCase
      - isSnakeCase
      - isFormattedForDatabaseUpload

  - title: "Record Keeping"
    desc: >
      Functions that support record keeping of tasks performed.
      CohortGenerator uses these functions when running in incremental
      mode to only generate cohorts when their definition has changed from
      a previous run.
    contents:
      - getRequiredTasks
      - recordTasksDone
      - isTaskRequired
      - saveIncremental
      - computeChecksum
      
  - title: "Cohort Sampling"
    desc: >
      Functions that support sampling a cohort. Please note this is only for
      software development purposes and NOT for running studies.
    contents:
      - sampleCohortDefinitionSet

navbar:
  bg: dark
  structure:
    right: [hades, github]
  components:
    hades:
      text: hadesLogo
      href: https://ohdsi.github.io/Hades