Identify Relevant Clinical Codes and Evaluate Their Use
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Documentation for package ‘CodelistGenerator’ version 3.5.0
Help Pages
| 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 |
| buildAchillesTables | Add the achilles tables with specified analyses |
| 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 |
| getATCCodes | Get the descendant codes of Anatomical Therapeutic Chemical (ATC) classification codes |
| 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 Classification of Diseases (ICD) 10 codes |
| 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 |
| mockVocabRef | Generate example vocabulary database |
| sourceCodesInUse | Get the source codes being used in patient records |
| 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 domain. |
| subsetOnDoseUnit | Subset a codelist to only those with a particular dose unit. |
| subsetOnRouteCategory | Subset a codelist to only those with a particular route category |
| 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 |
| 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. |
| tableOrphanCodes | Format the result of summariseOrphanCodes into a table |
| tableUnmappedCodes | Format the result of summariseUnmappedCodeUse into a table |