PhenotypeR (version 0.1.4)

codelistDiagnostics: 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)

Value

A summarised result

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.

Examples

# \donttest{
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)
# }