Package index • CodelistGenerator

getCandidateCodes(): Perform a systematic search to identify a candidate codelist using the OMOP CDM vocabulary tables.
searchStrategy(): Report the search strategy used to identify codes when using the getCandidateCodes() function

getDrugIngredientCodes(): Get descendant codes of drug ingredients
getATCCodes(): Get the descendant codes of Anatomical Therapeutic Chemical (ATC) classification codes

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 using achilles counts and, if available, PHOEBE concept recommendations

tableAchillesCodeUse(): Format the result of summariseAchillesCodeUse into a table
tableCodeUse(): Format the result of summariseCodeUse into a table.
tableCohortCodeUse(): Format the result of summariseCohortCodeUse into a table.
tableOrphanCodes(): Format the result of summariseOrphanCodes into a table

codesFromCohort(): Get concept ids from JSON files containing cohort definitions
codesFromConceptSet() deprecated: Get concept ids from JSON files containing concept sets

unionCodelists(): Generate a codelist from the union of different codelists. The generated codelist will come out in alphabetical order.
intersectCodelists(): Generate a codelist from the intersection of different codelists. The generated codelist will come out in alphabetical order.

subsetToCodesInUse(): Filter a codelist to keep only the codes being used in patient records
subsetOnRouteCategory(): Subset a codelist to only those with a particular route category
subsetOnDoseUnit(): Subset a codelist to only those with a particular dose unit.
subsetOnDomain(): Subset a codelist to only those codes from a particular domain.
subsetOnVocabulary(): Subset a codelist to only those codes from a particular vocabulary.
subsetOnIngredientRange(): Subset a codelist to only those codes with a range of number of ingredients
subsetOnDoseForm(): Subset a codelist to only those codes from a particular domain.

stratifyByRouteCategory(): Stratify a codelist by route category.
stratifyByDoseUnit(): Stratify a codelist by dose unit.
stratifyByDomain(): Stratify a codelist by domain category.
stratifyByVocabulary(): Subset a codelist to only those codes from a particular domain.
stratifyByDoseForm(): Stratify a codelist by dose form.
stratifyByConcept(): Stratify a codelist by the concepts included within it.
stratifyByBrand(): Stratify a codelist by brand category.

vocabularyVersion(): Get the available version of the vocabulary used in the cdm
getDescendants(): Get descendant codes for a given concept

availableATC(): Get the names of all available Anatomical Therapeutic Chemical (ATC) classification codes
availableConceptClassIds(): Get the available concept classes used in a given set of domains
availableDomains(): Get the domains available in the cdm
availableDoseForms(): Get the dose forms for drug concepts
availableDoseUnits(): Get available dose units
availableDrugIngredients(): Get the names of all available drug ingredients
availableRouteCategories(): Get available drug routes
availableRelationshipIds(): Get available relationships between concepts
availableVocabularies(): Get the available vocabularies available in the cdm

associatedConceptClassIds(): Get the concept classes associated with a codelist
associatedDomains(): Get the domains associated with a codelist
associatedDoseForms(): Get the dose forms associated with drug concepts in a codelist
associatedDoseUnits(): Get available dose units
associatedDrugIngredients(): Get the names of drug ingredients associated with codelist
associatedRouteCategories(): Get drug routes associated with a codelist
associatedRelationshipIds(): Get available relationships with concepts in a codelist
associatedVocabularies(): Get the vocabularies associated with a codelist

doseFormToRoute: Table showing the route category associated with each dose form.