Map source (non-standard) codes to their standard OMOP concepts

Uses the concept_relationship 'Maps to' relationship. SQL lives in inst/sql/mapSourceToStandard.sql.

mapSourceToStandard(
  sourceCodes,
  connection,
  vocabularyDatabaseSchema,
  vocabularyId = NULL
)

Arguments

sourceCodes

Character vector of source codes (e.g. ICD-10 codes).

connection

A DatabaseConnector connection to an OMOP CDM.

vocabularyDatabaseSchema

Schema containing the OMOP vocabulary tables. Required.

vocabularyId

Optional vocabulary IDs to restrict source lookup (e.g. "ICD10CM").

Value

A tibble with source and mapped standard concept columns.

See also

searchConcepts, cs, mapped

Examples

if (FALSE) {
connection <- DatabaseConnector::connect(Eunomia::getEunomiaConnectionDetails())
mapSourceToStandard(c("I48", "I48.0"), connection,
  vocabularyDatabaseSchema = "main", vocabularyId = "ICD10CM")
}