PhenotypeR (version 0.3.2)

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, measurementSample = 20000)

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.

measurementSample

The number of people to take a random sample for measurement diagnostics. If `measurementSample = NULL`, no sampling will be performed. If `measurementSample = 0` measurement diagnostics will not be run.

Examples

# \donttest{
library(omock)
library(CohortConstructor)
library(PhenotypeR)

cdm <- mockCdmFromDataset(source = "duckdb")
cdm$warfarin <- conceptCohort(cdm,
                              conceptSet =  list(warfarin = c(1310149L,
                                                              40163554L)),
                              name = "warfarin")
result <- codelistDiagnostics(cdm$warfarin)

CDMConnector::cdmDisconnect(cdm = cdm)
# }