summariseOrphanCodes: Find orphan codes related to a codelist using achilles counts...

In CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

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")
)

Arguments

x	A codelist for which to find related codes used in the database
cdm	cdm_reference via CDMConnector
domain	The domains to restrict results too. Only concepts from these domains will be returned.

Value

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

Examples

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)

CodelistGenerator documentation built on Oct. 17, 2024, 5:09 p.m.