Package index • CodelistGenerator

Search for codes following a systematic search strategy

getCandidateCodes(): Generate candidate codelist for the OMOP CDM

Create vocabulary-based codelists

getATCCodes(): Get descendant codes for ATC levels

getDrugIngredientCodes(): Get descendant codes for drug ingredients

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

Run codelist diagnostics

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

summariseUnmappedCodes(): Findunmapped concepts related to codelist

Present codelist diagnostics results in a table

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.

tableUnmappedCodes(): Format the result of summariseUnmappedCodeUse into a table.

Extract codelists from JSON files

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

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

Codelist utility functions

codesInUse(): Use achilles counts to get codes used in the database

compareCodelists(): Compare two codelists

stratifyByConcept(): Stratify a codelist by the concepts included within it

stratifyByDoseUnit(): Stratify a codelist by dose unit

stratifyByRouteCategory(): Stratify a codelist by route category

subsetOnDomain(): Subset a codelist to only those codes from a particular domain

subsetOnDoseUnit(): Subset a codelist to only those with a particular dose unit

subsetOnRouteCategory(): Subset a codelist to only those with a particular route category

subsetToCodesInUse(): Use achilles counts to filter a codelist to keep only the codes used in the database

Vocabulary utility functions

availableATC(): Get all ATC codes from the cdm

availableICD10(): Get all ICD codes from the cdm

availableIngredients(): Get all ingredients codes from the cdm

doseFormToRoute: Equivalence from dose from concept IDs to route categories.

getConceptClassId(): getConceptClassId

getDescendants(): getDescendants

getDomains(): getDomains

getDoseForm(): getDoseForm

getDoseUnit(): Get available routes in a cdm reference.

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

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

getRouteCategories(): Get available routes in a cdm reference.

getVocabVersion(): getVocabVersion

getVocabularies(): getVocabularies

sourceCodesInUse(): Use achilles counts to get source codes used in the database

Create a mock dataset that contains vocabulary tables

mockVocabRef(): Generate example vocabulary database