R: Identify Relevant Clinical Codes and Evaluate Their Use

# Identify Relevant Clinical Codes and Evaluate Their Use

## Documentation for package ‘CodelistGenerator’ version 4.0.2

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

## Help Pages

addConcepts | Add concepts to a codelist
asCodelist | Coerce to a codelist
asCodelist.candidate_codes | Coerce to a codelist
asCodelist.codelist | Coerce to a codelist
asCodelist.codelist_with_details | Coerce to a codelist
asCodelist.concept_set_expression | Coerce to a codelist
asCodelistWithDetails | Coerce to a codelist with details
asCodelistWithDetails.candidate_codes | Coerce to a codelist with details
asCodelistWithDetails.codelist | Coerce to a codelist with details
asCodelistWithDetails.codelist_with_details | Coerce to a codelist with details
asConceptSetExpression | Coerce to a concept set expression
asConceptSetExpression.codelist | Coerce to a concept set expression
asConceptSetExpression.codelist_with_details | Coerce to a concept set expression
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
associatedRelationshipIds | Get available relationships with concepts in a codelist
associatedRouteCategories | Get drug routes associated with a codelist
associatedVocabularies | Get the vocabularies associated with a codelist
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
availableRelationshipIds | Get available relationships between concepts
availableRouteCategories | Get available drug routes
availableVocabularies | Get the available vocabularies available in the cdm
benchmarkCodelistGenerator | Run benchmark of codelistGenerator analyses
codesFromCohort | Get concept ids from JSON files containing cohort definitions
codesFromConceptSet | Get concept ids from JSON files containing concept sets *[Deprecated]*
compareCodelists | Compare overlap between two sets of codes
doseFormToRoute | Table showing the route category associated with each dose form.
excludeConcepts | Exclude concepts from a codelist
getATCCodes | Get the descendant codes of Anatomical Therapeutic Chemical (ATC) classification codes
getCandidateCodes | Perform a systematic search to identify a candidate codelist using the OMOP CDM vocabulary tables.
getDescendants | Get descendant codes for a given concept
getDrugIngredientCodes | Get descendant codes of drug ingredients
getMappings | Show mappings from non-standard vocabularies to standard.
intersectCodelists | Generate a codelist from the intersection of different codelists. The generated codelist will come out in alphabetical order.
mockVocabRef | Generate example vocabulary database
searchStrategy | Report the search strategy used to identify codes when using the 'getCandidateCodes()' function
stratifyByBrand | Stratify a codelist by brand category.
stratifyByConcept | Stratify a codelist by the concepts included within it.
stratifyByDomain | Stratify a codelist by domain category.
stratifyByDoseForm | Stratify a codelist by dose form.
stratifyByDoseUnit | Stratify a codelist by dose unit.
stratifyByRouteCategory | Stratify a codelist by route category.
stratifyByVocabulary | Subset a codelist to only those codes from a particular domain.
subsetOnDomain | Subset a codelist to only those codes from a particular domain.
subsetOnDoseForm | Subset a codelist to only those codes from a particular domain.
subsetOnDoseUnit | Subset a codelist to only those with a particular dose unit.
subsetOnIngredientRange | Subset a codelist to only those codes with a range of number of ingredients
subsetOnRouteCategory | Subset a codelist to only those with a particular route category
subsetOnVocabulary | Subset a codelist to only those codes from a particular vocabulary.
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
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
unionCodelists | Generate a codelist from the union of different codelists. The generated codelist will come out in alphabetical order.
vocabularyVersion | Get the available version of the vocabulary used in the cdm