CodelistGenerator (version 4.0.0)

codesFromConceptSet: 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"))

Value

Named list with concept_ids for each concept set.

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".

Examples

# \donttest{
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

# }