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Run codelist-level diagnostics

Source: R/codelistDiagnostics.R
codelistDiagnostics.Rd

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,
  cohortId = NULL,
  achillesCodeUse = FALSE,
  orphanCodeUse = TRUE,
  cohortCodeUse = TRUE,
  drugDiagnostics = FALSE,
  drugDiagnosticsSample = 20000,
  measurementDiagnostics = FALSE,
  measurementDiagnosticsSample = 20000
)

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.

cohortId

Specific cohort definition ID for which to run codelist diagnostics.

achillesCodeUse

Whether to run CodelistGenerator::summariseAchillesCodeUse() (TRUE) or not (FALSE).

orphanCodeUse

Whether to run CodelistGenerator::summariseOrphanCodeUse() (TRUE) or not (FALSE).

cohortCodeUse

Whether to run CodelistGenerator::summariseCohortCodeUse() (TRUE) or not (FALSE).

drugDiagnostics

Whether to run drug diagnostics (TRUE) or not (FALSE). Note that, if set to TRUE, the diagnostics will only run if the cohort code list contains drug codes.

drugDiagnosticsSample

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

measurementDiagnostics

Whether to run measurement diagnostics (TRUE) or not (FALSE). Note that, if set to TRUE, the diagnostics will only run if the cohort code list contains measurement codes.

measurementDiagnosticsSample

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

Value

A summarised result

Examples

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

cdm <- mockCdmFromDataset(source = "duckdb")
#> ℹ Loading bundled GiBleed tables from package data.
#> 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 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)
# }