nprcgenekeepr (version 2.0.0)

runQcStudbook: Run Quality Control on Studbook with UI-Friendly Results

Description

Wrapper function that runs qcStudbook and processes results into a format suitable for Shiny UI display. This function performs two passes: first to check for errors, then to get the cleaned data if no errors exist.

Usage

runQcStudbook(
  ped,
  minSireAge = NULL,
  minDamAge = NULL,
  minParentAge = lifecycle::deprecated(),
  reportChanges = FALSE
)

Value

A list with the following components:

• cleaned - The cleaned pedigree data.frame with standardized column names, added generation numbers, etc. NULL if errors were found.

• qcResult - Result from processQcStudbookResult containing errors, warnings, changedCols, hasErrors, and hasChangedCols.

• errorLst - The raw nprcgenekeeprErr list from qcStudbook's first pass (the same object qcResult was derived from), exposed so callers that need the raw fields (e.g. femaleSires, failedDatabaseConnection) do not have to call qcStudbook a second time themselves.

Arguments

ped

data.frame containing pedigree data with columns including id, sire, dam, sex, and optionally birth, death, departure, etc.

minSireAge

numeric minimum age in years for a male to have sired an offspring. NULL (default) looks up each sire's species floor via getSpeciesMinBreedingAge (2 years when species is unknown); a supplied value overrides that floor.

minDamAge

numeric minimum age in years for a female to have borne an offspring. NULL (default) looks up each dam's species floor via getSpeciesMinBreedingAge (2 years when species is unknown); a supplied value overrides that floor.

minParentAge

Deprecated scalar minimum parent age. Supplying it sets both minSireAge and minDamAge; use those sex-specific parameters instead.

reportChanges

logical whether to report column name changes in the result (default FALSE). When TRUE, warnings about renamed columns are included in the qcResult.

See Also

qcStudbook for the underlying QC function

processQcStudbookResult for result processing

modInputServer for Shiny module integration

Examples

data("pedGood", package = "nprcgenekeepr")
result <- runQcStudbook(pedGood, minSireAge = 2.0, minDamAge = 2.0)
if (!result$qcResult$hasErrors) {
  cleanedPed <- result$cleaned
}