Subset a codelist to only those codes from a particular vocabulary.

Usage

subsetOnVocabulary(x, cdm, vocabulary, negate = FALSE)

Arguments

x: A codelist.
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).
vocabulary: Vocabulary to subset with (i.e., SNOMED)
negate: If FALSE, only concepts with the vocabulary specified will be returned. If TRUE, concepts with the vocabulary specified will be excluded.

Value

The codelist with only those concepts associated with the vocabulary (if negate = FALSE) or the codelist without those concepts associated with the vocabulary (if negate = TRUE).

Examples

# \donttest{
library(CodelistGenerator)
library(omopgenerics)
cdm <- mockVocabRef()
codes <- subsetOnVocabulary(
              x = newCodelist(list("codes" = c(1L,13L,15L))),
              cdm = cdm,
              vocabulary = "SNOMED")
codes
#> 
#> ── 1 codelist ──────────────────────────────────────────────────────────────────
#> 
#> - codes (1 codes)
# }