subsetToCodesInUse: Filter a codelist to keep only the codes being used in...

In CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

Filter a codelist to keep only the codes being used in patient records

Description

Filter a codelist to keep only the codes being used in patient records

Usage

subsetToCodesInUse(
  x,
  cdm,
  minimumCount = 0L,
  table = c("condition_occurrence", "device_exposure", "drug_exposure", "measurement",
    "observation", "procedure_occurrence", "visit_occurrence")
)

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).
minimumCount	Any codes with a frequency under this will be removed.
table	cdm table of interest.

Value

The filtered codelist with only the codes used in the database

Examples

library(CodelistGenerator)
library(omopgenerics)
cdm <- mockVocabRef("database")
codes <- getCandidateCodes(cdm = cdm,
                           keywords = "arthritis",
                           domains = "Condition",
                           includeDescendants = FALSE)
x <- subsetToCodesInUse(newCodelist(list("cs1" = codes$concept_id,
                               "cs2" = 999)),
                                cdm = cdm)

x
CDMConnector::cdmDisconnect(cdm)

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