CodelistGenerator/_pkgdown.yml at main · darwin-eu/CodelistGenerator · GitHub

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

navbar:
  structure:
    right: [github]

articles:
- title: OMOP CDM vocabularies
  navbar: OMOP CDM vocabularies
  contents:
  - a01_GettingOmopCdmVocabularies
  - a02_ExploreCDMvocabulary
  - a03_TypesOfCodelist
  - a06_ImportExport
- title: Finding codes
  navbar: Finding codes
  contents:
  - a04_GenerateCandidateCodelist
  - a05_GenerateVocabularyBasedCodelist
  - a08_ManipulateCodelists
- title: Codelist diagnostics
  navbar: Codelist diagnostics
  contents:
  - a09_RunCodelistDiagnostics
- title: Package benchmark
  navbar: Package benchmark
  contents:
  - a10_CodelistGeneratorBenchmark

reference:
- subtitle: Search for codes following a systematic search strategy
- contents:
  - getCandidateCodes
  - searchStrategy
  - exportCodeSearch
  - importCodeSearch
  - newCodeSearch
  - emptyCodeSearch
- subtitle: Create vocabulary-based codelists
- contents:
  - getDrugIngredientCodes
  - getATCCodes
- subtitle: Run codelist diagnostics
- contents:
  - summariseAchillesCodeUse
  - summariseCodeUse
  - summariseCohortCodeUse
  - summariseOrphanCodes
- subtitle: Present codelist diagnostics results in a table
- contents:
  - tableAchillesCodeUse
  - tableCodeUse
  - tableCohortCodeUse
  - tableOrphanCodes
- subtitle: Extract codelists from JSON files
- contents:
  - codesFromCohort
  - codesFromConceptSet
- subtitle: Combine codelists
- contents:
  - unionCodelists
  - intersectCodelists
- subtitle: Subset codelists
- contents:
  - subsetToCodesInUse
  - subsetOnRouteCategory
  - subsetOnDoseUnit
  - subsetOnDomain
  - subsetOnVocabulary
  - subsetOnIngredientRange
  - subsetOnDoseForm
- subtitle: Stratify codelists
- contents:
  - stratifyByRouteCategory
  - stratifyByDoseUnit
  - stratifyByDomain
  - stratifyByVocabulary
  - stratifyByDoseForm
  - stratifyByConcept
  - stratifyByBrand
- subtitle: Codelist utility functions
- contents:
  - addConcepts
  - excludeConcepts
  - compareCodelists
  - getMappings
  - asCodelist
  - asCodelistWithDetails
  - asConceptSetExpression
- subtitle: Vocabulary utility functions
- contents:
  - vocabularyVersion
  - getDescendants
- subtitle: Identify concepts available in the OMOP CDM
- contents:
  - availableATC
  - availableConceptClassIds
  - availableDomains
  - availableDoseForms
  - availableDoseUnits
  - availableDrugIngredients
  - availableRouteCategories
  - availableRelationshipIds
  - availableVocabularies
- subtitle: Identify concepts associated with a codelist
- contents:
  - associatedConceptClassIds
  - associatedDomains
  - associatedDoseForms
  - associatedDoseUnits
  - associatedDrugIngredients
  - associatedRouteCategories
  - associatedRelationshipIds
  - associatedVocabularies
- subtitle: Datasets
- contents:
  - doseFormToRoute
- subtitle: Benchmark
- contents:
  - benchmarkCodelistGenerator
- subtitle: Create a mock dataset that contains vocabulary tables
- contents:
  - mockVocabRef