Function reference • CodelistGenerator

All functions

codesFromCohort(): Get concept ids from a provided path to cohort json files

codesFromConceptSet(): Get concept ids from a provided path to json files

codesInUse(): Get codes used in the database

compareCodelists(): Compare two codelists

getATCCodes(): Get descendant codes for ATC levels

getCandidateCodes(): Generate candidate codelist for the OMOP CDM

getConceptClassId(): getConceptClassId

getDescendants(): getDescendants

getDomains(): getDomains

getDoseForm(): getDoseForm

getDrugIngredientCodes(): Get descendant codes for drug ingredients

getICD10StandardCodes(): Get corresponding standard codes for ICD-10 chapters and sub-chapters

getMappings(): Show mappings from non-standard vocabularies to standard

getRelationshipId(): Get relationship ID values from the concept relationship table

getVocabVersion(): getVocabVersion

getVocabularies(): getVocabularies

mockVocabRef(): Generate example vocabulary database

restrictToCodesInUse(): Filter a codelist to keep only the codes used in the database

sourceCodesInUse(): Get source codes used in the database

summariseAchillesCodeUse(): Summarise code use from achilles counts

summariseCodeUse(): Summarise code use in patient-level data

summariseCohortCodeUse(): Summarise code use among a cohort in the cdm reference

summariseOrphanCodes(): Find orphan codes related to a codelist

tableAchillesCodeUse(): Format the result of summariseAchillesCodeUse into a visual table.

tableCodeUse(): Format the result of summariseCodeUse into a visual table.

tableCohortCodeUse(): Format the result of summariseCohortCodeUse into a visual table.

tableOrphanCodes(): Format the result of summariseOrphanCodes into a visual table.