Run codelist-level diagnostics

`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

# \donttest{
  cdm_local <- omock::mockCdmReference() |>
  omock::mockPerson(nPerson = 100) |>
  omock::mockObservationPeriod() |>
  omock::mockConditionOccurrence() |>
  omock::mockDrugExposure() |>
  omock::mockCohort(name = "my_cohort")

  db <- DBI::dbConnect(duckdb::duckdb())

  cdm <- CDMConnector::copyCdmTo(con = db,
                                 cdm = cdm_local,
                                 schema ="main",
                                 overwrite = TRUE)

 result <- cdm$my_cohort |>
   codelistDiagnostics()
#> • Getting codelists from cohorts
#> Warning: No codelists found for the specified cohorts
#> Warning: Empty cohort_codelist attribute for cohort
#> ℹ Returning an empty summarised result

 CDMConnector::cdmDisconnect(cdm = cdm)
# }