Concept sets created in R using the `cs` function do not contain details like "CONCEPT_NAME", "DOMAIN_ID", etc. If an OMOP CDM vocabulary is available then these details can be filled in by the the `getConceptSetDetails` function.
getConceptSetDetails(x, con, vocabularyDatabaseSchema = NULL)Arguments
- x
A concept set created by `cs`
- con
A connection to an OMOP CDM database
- vocabularyDatabaseSchema
Schema name where your OMOP vocabulary format resides. Note that for SQL Server, this should include both the database and schema name, for example 'vocabulary.dbo'.
Value
A modified version of the input concept set with concept details filled in.
Examples
if (FALSE) {
# create a concept set
vocabularyDatabaseSchema = "cdm5"
anemia <- cs(descendants(439777,4013073,4013074), name = "anemia")
# fill in the details from an OMOP CDM
library(DatabaseConnector)
con <- connect(dbms = "postgresql", user = "postgres", password = "", server = "localhost/cdm")
anemia <- getConceptSetDetails(condition_anemia, con, vocabularyDatabaseSchema = "cdm5")
}