_pkgdown.yml

template:
  params:
    bootswatch: cosmo

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

reference:
  - 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 Generation"
    desc: >
      Functions that support generating cohorts.
    contents:
      - generateCohortSet
      - createEmptyCohortDefinitionSet
      
  - title: "Cohort Counts"
    desc: >
      Function for obtaining the counts of subjects and events for one or
      more cohorts
    contents:
      - getCohortCounts
      
  - 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.
    contents:
      - getCohortStats
      - 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: "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

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