codelistDiagnostics: Run codelist-level diagnostics

In PhenotypeR: Assess Study Cohorts Using a Common Data Model

Run codelist-level diagnostics

Description

'codelistDiagnostics()' runs phenotypeR diagnostics on the cohort_codelist attribute on the cohort. Thus codelist attribute of the cohort must be populated. If it is missing then it could be populated using 'addCodelistAttribute()' function.

Furthermore 'codelistDiagnostics()' requires achilles tables to be present in the cdm so that concept counts could be derived.

Usage

codelistDiagnostics(cohort)

Arguments

cohort

A cohort table in a cdm reference. The cohort_codelist attribute must be populated. The cdm reference must contain achilles tables as these will be used for deriving concept counts.

Value

A summarised result

Examples

library(CohortConstructor)
library(PhenotypeR)

cdm <- mockPhenotypeR()

cdm$arthropathies <- conceptCohort(cdm,
                                   conceptSet = list("arthropathies" = c(40475132)),
                                   name = "arthropathies")

result <- codelistDiagnostics(cdm$arthropathies)

CDMConnector::cdmDisconnect(cdm = cdm)

PhenotypeR documentation built on April 3, 2025, 10:46 p.m.