CodelistGenerator (version 3.5.0)

summariseOrphanCodes: Find orphan codes related to a codelist using achilles counts and, if available, PHOEBE concept recommendations

Description

Find orphan codes related to a codelist using achilles counts and, if available, PHOEBE concept recommendations

Usage

summariseOrphanCodes(
  x,
  cdm,
  domain = c("condition", "device", "drug", "measurement", "observation", "procedure",
    "visit")
)

Value

A summarised result containg the frequency of codes related to (but not in) the codelist.

Arguments

x

A codelist.

cdm

A cdm reference via CDMConnector.

domain

Character vector with one or more of the OMOP CDM domains. The results will be restricted to the given domains. Check the available ones by running getDomains(). If NULL, all supported domains are included: Condition, Drug, Procedure, Device, Observation, and Measurement.

Examples

# \donttest{
cdm <- mockVocabRef("database")
codes <- getCandidateCodes(cdm = cdm,
keywords = "Musculoskeletal disorder",
domains = "Condition",
includeDescendants = FALSE)

orphan_codes <- summariseOrphanCodes(x = list("msk" = codes$concept_id),
cdm = cdm)

orphan_codes
CDMConnector::cdmDisconnect(cdm)
# }