subsetOnVocabulary: Subset a codelist to only those codes from a particular...

In CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

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

Description

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

library(CodelistGenerator)
library(omopgenerics)
cdm <- mockVocabRef()
codes <- subsetOnVocabulary(
              x = newCodelist(list("codes" = c(1L,13L,15L))),
              cdm = cdm,
              vocabulary = "SNOMED")
codes

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