Man pages for CodelistGenerator
Identify Relevant Clinical Codes and Evaluate Their Use
| addConcepts | Add concepts to a codelist |
| ageGroupDoc | Helper for consistent documentation of 'ageGroup'. |
| asCodelist | Coerce to a codelist |
| asCodelistWithDetails | Coerce to a codelist with details |
| asConceptSetExpression | 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... |
| 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... |
| availableConceptClassIds | Get the available concept classes used in a given set of... |
| 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 |
| byConceptDoc | Helper for consistent documentation of 'byConcept'. |
| bySexDoc | Helper for consistent documentation of 'bySex'. |
| byYearDoc | Helper for consistent documentation of 'byYear'. |
| cdmDoc | Helper for consistent documentation of 'cdm'. |
| CodelistGenerator-package | CodelistGenerator: Identify Relevant Clinical Codes and... |
| codelistNameDoc | Helper for consistent documentation of 'codelistNameDoc' |
| codesFromCohort | Get concept ids from JSON files containing cohort definitions |
| codesFromConceptSet | Get concept ids from JSON files containing concept sets... |
| compareCodelists | Compare overlap between two sets of codes |
| countByDoc | Helper for consistent documentation of 'countBy'. |
| domainDoc | Helper for consistent documentation of 'domain'. |
| doseFormDoc | Helper for consistent documentation of 'doseForm'. |
| doseFormToRoute | Table showing the route category associated with each dose... |
| doseUnitDoc | Helper for consistent documentation of 'doseUnit'. |
| dot-optionsDoc | Helper for consistent documentation of '.options'. |
| excludeConcepts | Exclude concepts from a codelist |
| getATCCodes | Get the descendant codes of Anatomical Therapeutic Chemical... |
| getCandidateCodes | Perform a systematic search to identify a candidate codelist... |
| getDescendants | Get descendant codes for a given concept |
| getDrugIngredientCodes | Get descendant codes of drug ingredients |
| getMappings | Show mappings from non-standard vocabularies to standard. |
| groupColumnDoc | Helper for consistent documentation of 'groupColumn'. |
| groupColumnStrataDoc | Helper for consistent documentation of 'groupColumn'. |
| headerDoc | Helper for consistent documentation of 'header'. |
| headerStrataDoc | Helper for consistent documentation of 'header'. |
| hideDoc | Helper for consistent documentation of 'hide'. |
| hideStrataDoc | Helper for consistent documentation of 'hide'. |
| includeDescendantsDoc | Helper for consistent documentation of 'includeDescendants'. |
| ingredientRangeDoc | Helper for consistent documentation of 'ingredientRange'. |
| intersectCodelists | Generate a codelist from the intersection of different... |
| keepOriginalDoc | Helper for consistent documentation of 'keepOriginal'. |
| keepOriginalDocSubset | Helper for consistent documentation of 'keepOriginal'. |
| levelATCDoc | Helper for consistent documentation of 'level'. |
| levelICD10Doc | Helper for consistent documentation of 'level'. |
| minimumCountDoc | Helper for consistent documentation of 'minimumCount'. |
| mockVocabRef | Generate example vocabulary database |
| nameStyleDoc | Helper for consistent documentation of 'nameStyle'. |
| reexports | Objects exported from other packages |
| routeCategoryDoc | Helper for consistent documentation of 'routeCategory'. |
| searchStrategy | Report the search strategy used to identify codes when using... |
| standardConceptDoc | Helper for consistent documentation of 'standardConcept'. |
| 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... |
| subsetOnDomain | Subset a codelist to only those codes from a particular... |
| subsetOnDoseForm | Subset a codelist to only those codes from a particular... |
| 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... |
| subsetOnRouteCategory | Subset a codelist to only those with a particular route... |
| subsetOnVocabulary | Subset a codelist to only those codes from a particular... |
| subsetToCodesInUse | Filter a codelist to keep only the codes being used in... |
| 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... |
| 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. |
| tableDoc | Helper for consistent documentation of 'table'. |
| tableOrphanCodes | Format the result of summariseOrphanCodes into a table |
| tableStyleDoc | Helper for consistent documentation of 'style'. |
| typeBroadDoc | Helper for consistent documentation of 'type'. |
| typeNarrowDoc | Helper for consistent documentation of 'type'. |
| typeTableDoc | Helper for consistent documentation of 'type'. |
| unionCodelists | Generate a codelist from the union of different codelists.... |
| vocabularyVersion | Get the available version of the vocabulary used in the cdm |
| xDoc | Helper for consistent documentation of 'x'. |
| xDocCohort | Helper for consistent documentation of 'x' where input can be... |
