_pkgdown.yml

url: https://darwin-eu.github.io/CodelistGenerator/
template:
  bootstrap: 5
  bootswatch: flatly

navbar:
  structure:
    right: [github]

reference:
- subtitle: Search for codes following a systematic search strategy
- contents:
  - matches("getCandidateCodes")
- subtitle: Create vocabulary-based codelists
- contents:
  - matches("getDrugIngredientCodes|getATCCodes|getICD10StandardCodes")
- subtitle: Run codelist diagnostics
- contents:
  - matches("summariseAchillesCodeUse|summariseCodeUse|summariseCohortCodeUse|summariseOrphanCodes|summariseUnmappedCodes")
- subtitle: Present codelist diagnostics results in a table
- contents:
  - matches("tableAchillesCodeUse|tableCodeUse|tableCohortCodeUse|tableOrphanCodes|tableUnmappedCodes")
- subtitle: Extract codelists from JSON files
- contents:
  - matches("codesFromCohort|codesFromConceptSet")
- subtitle: Codelist utility functions
- contents:
  - matches("codesInUse|compareCodelists|subsetToCodesInUse|restrictToCodesInUse|subsetOnRouteCategory|stratifyByRouteCategory|stratifyByDoseUnit|stratifyByConcept|subsetOnDoseUnit|subsetOnDomain")
- subtitle: Vocabulary utility functions
- contents:
  - matches("getVocabVersion|getVocabularies|getConceptClassId|getDomains|getDescendants|getDoseForm|doseFormToRoute|getRouteCategories|getRoutes|getDoseUnit|getRelationshipId|getMappings|sourceCodesInUse|availableATC|availableICD10|availableIngredients")
- subtitle: Create a mock dataset that contains vocabulary tables
- contents:
  - matches("mockVocabRef")