# Identify Relevant Clinical Codes and Evaluate Their Use

## Documentation for package ‘CodelistGenerator’ version 3.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

availableATC | Get the names of all available Anatomical Therapeutic Chemical (ATC) classification codes
availableICD10 | Get the names of all International Classification of Diseases (ICD) 10 codes
availableIngredients | Get the names of all available drug ingredients
buildAchillesTables | Add the achilles tables with specified analyses
codesFromCohort | Get concept ids from JSON files containing cohort definitions
codesFromConceptSet | Get concept ids from JSON files containing concept sets
codesInUse | Get the concepts being used in patient records
compareCodelists | Compare overlap between two sets of codes
getATCCodes | Get the descendant codes of Anatomical Therapeutic Chemical (ATC) classification codes
getCandidateCodes | Generate a candidate codelist
getConceptClassId | Get the concept classes used in a given set of domains
getDescendants | Get descendant codes for a given concept
getDomains | Get the domains available in the cdm
getDoseForm | Get the dose forms available for drug concepts
getDoseUnit | Get available dose units
getDrugIngredientCodes | Get descendant codes of drug ingredients
getICD10StandardCodes | Get corresponding standard codes for International Classification of Diseases (ICD) 10 codes
getMappings | Show mappings from non-standard vocabularies to standard.
getRelationshipId | Get available relationships between concepts
getRouteCategories | Get available drug routes
getVocabularies | Get the vocabularies available in the cdm
getVocabVersion | Get the version of the vocabulary used in the cdm
mockVocabRef | Generate example vocabulary database
sourceCodesInUse | Get the source codes being used in patient records
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 | Filter a codelist to keep only the codes being used in patient records
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 | Find unmapped concepts related to codelist
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