codesFromConceptSet: Get concept ids from JSON files containing concept sets...

In CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

Get concept ids from JSON files containing concept sets

Description

Get concept ids from JSON files containing concept sets

Usage

codesFromConceptSet(path, cdm, type = c("codelist"))

Arguments

path	Path to a file or folder containing JSONs of concept sets.
cdm	A cdm reference to an OMOP CDM dataset. If data is held within a database, the vocabulary tables should be in the same schema as the clinical tables (person, observation period, and so on).
type	Can be "codelist", "codelist_with_details" or "concept_set_expression".

Value

Named list with concept_ids for each concept set.

Examples

library(CodelistGenerator)
library(omock)

# Create a CDM object
cdm <- mockCdmReference()

# Load JSON files
x <- codesFromConceptSet(cdm = cdm,
                         path =  system.file(package = "CodelistGenerator",
                                             "concepts_for_mock"))
x

# Load JSON files as codelist_with_details
x <- codesFromConceptSet(cdm = cdm,
                         path =  system.file(package = "CodelistGenerator",
                                             "concepts_for_mock"),
                         type = "codelist_with_details")
x

# Load JSON files as concept_set_expression
x <- codesFromConceptSet(cdm = cdm,
                         path =  system.file(package = "CodelistGenerator",
                                             "concepts_for_mock"),
                         type = "concept_set_expression")
x

CodelistGenerator documentation built on Dec. 17, 2025, 5:06 p.m.