nprcgenekeepr (version 2.0.0)

summary.nprcgenekeeprErr: Summarize a studbook quality-control error list

Description

Summarize a studbook quality-control error list

Usage

# S3 method for nprcgenekeeprErr
summary(object, ...)
# S3 method for nprcgenekeeprGV
summary(object, ...)

Value

Object of class summary.nprcgenekeeprErr

object of class summary.nprcgenekeeprGV

Arguments

object

object of class nprcgenekeeprErr and class list

...

additional arguments for the summary.default statement

Examples

errorList <- qcStudbook(nprcgenekeepr::pedOne,
  minParentAge = 0,
  reportChanges = TRUE,
  reportErrors = TRUE
)
summary(errorList)
examplePedigree <- nprcgenekeepr::examplePedigree
breederPed <- qcStudbook(examplePedigree,
  minParentAge = 2L,
  reportChanges = FALSE,
  reportErrors = FALSE
)
focalAnimals <- breederPed$id[!(is.na(breederPed$sire) &
  is.na(breederPed$dam)) &
  is.na(breederPed$exit)]
ped <- setPopulation(ped = breederPed, ids = focalAnimals)
trimmedPed <- trimPedigree(focalAnimals, breederPed)
probands <- ped$id[ped$population]
ped <- trimPedigree(probands, ped,
  removeUninformative = FALSE,
  addBackParents = FALSE
)
geneticValue <- reportGV(ped,
  guIter = 50L, # should be >= 1000L
  guThresh = 3L,
  byID = TRUE,
  updateProgress = NULL
)
trimmedGeneticValue <- reportGV(trimmedPed,
  guIter = 50L, # should be >= 1000L
  guThresh = 3L,
  byID = TRUE,
  updateProgress = NULL
)
summary(geneticValue)
summary(trimmedGeneticValue)