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{
library(omock)
library(CohortConstructor)
library(PhenotypeR)

cdm <- mockCdmFromDataset(source = "duckdb")
#> ℹ Reading GiBleed tables.
#> ℹ Adding drug_strength table.
#> ℹ Creating local <cdm_reference> object.
#> ℹ Inserting <cdm_reference> into duckdb.
cdm$warfarin <- conceptCohort(cdm,
                              conceptSet =  list(warfarin = c(1310149L,
                                                              40163554L)),
                              name = "warfarin")
#> ℹ Subsetting table drug_exposure using 2 concepts with domain: drug.
#> ℹ Combining tables.
#> ℹ Creating cohort attributes.
#> ℹ Applying cohort requirements.
#> ℹ Merging overlapping records.
#> ✔ Cohort warfarin created.
result <- codelistDiagnostics(cdm$warfarin)
#> • Getting codelists from cohorts
#> • Getting index event breakdown
#> Getting counts of warfarin codes for cohort warfarin
#> Warning: The CDM reference containing the cohort must also contain achilles tables.
#> Returning only index event breakdown.

CDMConnector::cdmDisconnect(cdm = cdm)
# }