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 sub-chapters |
getMappings |
Show mappings from non-standard vocabularies to standard |
getRelationshipId |
Get relationship ID values from the concept relationship table |
getRouteCategories |
Get available routes in a cdm reference. |
getVocabularies |
getVocabularies |
getVocabVersion |
getVocabVersion |
mockVocabRef |
Generate example vocabulary database |
restrictToCodesInUse |
Use achilles counts to filter a codelist to keep only the codes used in the database |
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 category |
subsetToCodesInUse |
Use achilles counts to filter a codelist to keep only the codes used in the database |
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 |
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. |