CodelistGenerator (version 4.0.0)

codesFromCohort: Get concept ids from JSON files containing cohort definitions

Description

Get concept ids from JSON files containing cohort definitions

Usage

codesFromCohort(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 cohort definitions.

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)
cdm <- mockVocabRef("database")
x <- codesFromCohort(cdm = cdm,
                     path =  system.file(package = "CodelistGenerator",
                     "cohorts_for_mock"))
x
CDMConnector::cdmDisconnect(cdm)
# }