Package index • CodelistGenerator

Search for codes following a systematic search strategy

getCandidateCodes(): Generate a candidate codelist

Create vocabulary-based codelists

getDrugIngredientCodes(): Get descendant codes of drug ingredients

getATCCodes(): Get the descendant codes of Anatomical Therapeutic Chemical (ATC) classification codes

getICD10StandardCodes(): Get corresponding standard codes for International Classification of Diseases (ICD) 10 codes

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(): Find unmapped 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 JSON files containing cohort definitions

codesFromConceptSet(): Get concept ids from JSON files containing concept sets

Codelist utility functions

compareCodelists(): Compare overlap between two sets of codes

subsetToCodesInUse(): Filter a codelist to keep only the codes being used in patient records

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

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

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

stratifyByRouteCategory(): Stratify a codelist by route category.

stratifyByDoseUnit(): Stratify a codelist by dose unit.

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

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

Vocabulary utility functions

getVocabVersion(): Get the version of the vocabulary used in the cdm

getVocabularies(): Get the vocabularies available in the cdm

getConceptClassId(): Get the concept classes used in a given set of domains

getDomains(): Get the domains available in the cdm

getDescendants(): Get descendant codes for a given concept

getDoseForm(): Get the dose forms available for drug concepts

getRouteCategories(): Get available drug routes

getDoseUnit(): Get available dose units

getRelationshipId(): Get available relationships between concepts

codesInUse(): Get the concepts being used in patient records

sourceCodesInUse(): Get the source codes being used in patient records

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

Create a mock dataset that contains vocabulary tables

mockVocabRef(): Generate example vocabulary database

buildAchillesTables(): Add the achilles tables with specified analyses