Get concept ids from JSON files containing cohort definitions

Usage

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

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".

Value

Named list with concept_ids for each concept set.

Examples

# \donttest{
library(CodelistGenerator)
cdm <- mockVocabRef("database")
x <- codesFromCohort(cdm = cdm,
                     path =  system.file(package = "CodelistGenerator",
                     "cohorts_for_mock"))
x
#> 
#> ── 3 codelists ─────────────────────────────────────────────────────────────────
#> 
#> - OA no descendants (1 codes)
#> - Other (1 codes)
#> - arthritis (3 codes)
CDMConnector::cdmDisconnect(cdm)
# }