# Identify Relevant Clinical Codes and Evaluate Their Use

## Documentation for package ‘CodelistGenerator’ version 3.3.0

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

## Help Pages

availableATC | Get all ATC codes from the cdm
availableICD10 | Get all ICD codes from the cdm
availableIngredients | Get all ingredients codes from the cdm
codesFromCohort | Get concept ids from a provided path to cohort json files
codesFromConceptSet | Get concept ids from a provided path to json files
codesInUse | Use achilles counts to get codes used in the database
compareCodelists | Compare two codelists
doseFormToRoute | Equivalence from dose from concept IDs to route categories.
getATCCodes | Get descendant codes for ATC levels
getCandidateCodes | Generate candidate codelist for the OMOP CDM
getConceptClassId | getConceptClassId
getDescendants | getDescendants
getDomains | getDomains
getDoseForm | getDoseForm
getDoseUnit | Get available routes in a cdm reference.
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
getRouteCategories | Get available routes in a cdm reference.
getVocabularies | getVocabularies
getVocabVersion | getVocabVersion
mockVocabRef | Generate example vocabulary database
sourceCodesInUse | Use achilles counts to get source codes used in the database
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
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
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.