Man pages for oxford-pharmacoepi/CodelistGenerator
Identify Relevant Clinical Codes and Evaluate Their Use
| CodelistGenerator-package | CodelistGenerator: Identify Relevant Clinical Codes and... |
| codesFromCohort | Get concept ids from a provided path to cohort json files |
| codesFromConceptSet | Get concept ids from a provided path to json files |
| codesInUse | Use achilles counts to get codes used in the database |
| compareCodelists | Compare two codelists |
| doseFormToRoute | Equivalence from dose from concept IDs to route categories. |
| getATCCodes | Get descendant codes for ATC levels |
| getCandidateCodes | Generate candidate codelist for the OMOP CDM |
| getConceptClassId | getConceptClassId |
| getDescendants | getDescendants |
| getDomains | getDomains |
| getDoseForm | getDoseForm |
| getDoseUnit | Get available routes in a cdm reference. |
| getDrugIngredientCodes | Get descendant codes for drug ingredients |
| getICD10StandardCodes | Get corresponding standard codes for ICD-10 chapters and... |
| getMappings | Show mappings from non-standard vocabularies to standard |
| getRelationshipId | Get relationship ID values from the concept relationship... |
| getRouteCategories | Get available routes in a cdm reference. |
| getVocabularies | getVocabularies |
| getVocabVersion | getVocabVersion |
| mockVocabRef | Generate example vocabulary database |
| pipe | Pipe operator |
| restrictToCodesInUse | Use achilles counts to filter a codelist to keep only the... |
| sourceCodesInUse | Use achilles counts to get source codes used in the database |
| stratifyByConcept | Stratify a codelist by the concepts included within it |
| stratifyByDoseUnit | Stratify a codelist by dose unit |
| stratifyByRouteCategory | Stratify a codelist by route category |
| subsetOnDoseUnit | Subset a codelist to only those with a particular dose unit |
| subsetOnRouteCategory | Subset a codelist to only those with a particular route... |
| subsetToCodesInUse | Use achilles counts to filter a codelist to keep only the... |
| 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. |
| tableOrphanCodes | Format the result of summariseOrphanCodes into a table. |
