codelistDiagnostics {PhenotypeR} | R Documentation |
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)
[Package PhenotypeR version 0.1.5 Index]