Identify Relevant Clinical Codes and Evaluate Their Use

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Documentation for package ‘CodelistGenerator’ version 4.0.1

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

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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