Man pages for CodelistGenerator
Identify Relevant Clinical Codes and Evaluate Their Use
| ageGroupDoc | Helper for consistent documentation of 'ageGroup'. |
| availableATC | Get the names of all available Anatomical Therapeutic... |
| availableICD10 | Get the names of all International Classification of Diseases... |
| availableIngredients | Get the names of all available drug ingredients |
| buildAchillesTables | Add the achilles tables with specified 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... |
| codesFromCohort | Get concept ids from JSON files containing cohort definitions |
| codesFromConceptSet | Get concept ids from JSON files containing concept sets |
| codesInUse | Get the concepts being used in patient records |
| 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'. |
| doseUnitDoc | Helper for consistent documentation of 'doseUnit'. |
| dot-optionsDoc | Helper for consistent documentation of '.options'. |
| getATCCodes | Get the descendant codes of Anatomical Therapeutic Chemical... |
| getCandidateCodes | Generate a candidate codelist |
| getConceptClassId | Get the concept classes used in a given set of domains |
| getDescendants | Get descendant codes for a given concept |
| getDomains | Get the domains available in the cdm |
| getDoseForm | Get the dose forms available for drug concepts |
| getDoseUnit | Get available dose units |
| getDrugIngredientCodes | Get descendant codes of drug ingredients |
| getICD10StandardCodes | Get corresponding standard codes for International... |
| getMappings | Show mappings from non-standard vocabularies to standard. |
| getRelationshipId | Get available relationships between concepts |
| getRouteCategories | Get available drug routes |
| getVocabularies | Get the vocabularies available in the cdm |
| getVocabVersion | Get the version of the vocabulary used in the cdm |
| 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'. |
| keepOriginalDoc | 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'. |
| sourceCodesInUse | Get the source codes being used in patient records |
| standardConceptDoc | Helper for consistent documentation of 'standardConcept'. |
| 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... |
| subsetOnDoseUnit | Subset a codelist to only those with a particular dose unit. |
| subsetOnRouteCategory | Subset a codelist to only those with a particular route... |
| 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... |
| summariseUnmappedCodes | Find unmapped 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. |
| tableDoc | Helper for consistent documentation of 'table'. |
| tableOrphanCodes | Format the result of summariseOrphanCodes into a table |
| tableUnmappedCodes | Format the result of summariseUnmappedCodeUse into a table |
| typeBroadDoc | Helper for consistent documentation of 'type'. |
| typeNarrowDoc | Helper for consistent documentation of 'type'. |
| typeTableDoc | Helper for consistent documentation of 'type'. |
| xDoc | Helper for consistent documentation of 'x'. |
