getConceptSetDetails: Fill in Concept Set details using a vocab

In OHDSI/Capr: Cohort Definition Application Programming

Fill in Concept Set details using a vocab

Description

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.

Usage

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

## Not run: 
# 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")

## End(Not run)

OHDSI/Capr documentation built on Feb. 20, 2025, 4 a.m.