Summarize a studbook quality-control error list

Summarizes either a studbook quality-control error list (class nprcgenekeeprErr) or a genetic value report (class nprcgenekeeprGV); this page covers both methods.

Usage

# S3 method for class 'nprcgenekeeprErr'
summary(object, ...)

# S3 method for class 'nprcgenekeeprGV'
summary(object, ...)

Arguments

object

object of class nprcgenekeeprErr or nprcgenekeeprGV

...

currently unused by either method

Value

For an error list, an object of class summary.nprcgenekeeprErr. It is a list with the elements txt (a character string describing the problems found) and sp (the data frame of suspicious parents).

For a genetic value report, a character vector of class summary.nprcgenekeeprGV

Examples

errorList <- qcStudbook(nprcgenekeepr::pedOne,
  minSireAge = 0,
  minDamAge = 0,
  reportChanges = TRUE,
  reportErrors = TRUE
)
summary(errorList)
#> Error: The animal listed as a sire and also listed as a female is: s1.
#> Error: The animal listed as a dam and also listed as a male is: d1.
#> Change: The column where period was removed is: sire.id to sireid.
#> Change: The columns where underscore was removed are: ego_id, dam_id, and birth_date to egoid, damid, and birthdate.
#> Change: The column changed from: egoid to id.
#> Change: The column changed from: sireid to sire.
#> Change: The column changed from: damid to dam.
#> Change: The column changed from: birthdate to birth.
#> 
#> Please check and correct the pedigree file.
#>  
#> Animal records where parent records are suspicious because of dates.
#> One or more parents appear too young at time of birth.
#>   dam sire id sex      birth recordStatus placeholder exit  sireBirth
#> 2  d2   s1 o2   F 2009-03-17     original       FALSE <NA> 2000-07-18
#> 3  d2   s2 o3   F 2012-04-11     original       FALSE <NA> 2006-06-19
#> 4  d2   s2 o4   M 2006-04-13     original       FALSE <NA> 2006-06-19
#>     damBirth sireAge damAge
#> 2 2015-09-16    8.66   -6.5
#> 3 2015-09-16    5.81   -3.4
#> 4 2015-09-16   -0.18   -9.4
examplePedigree <- nprcgenekeepr::examplePedigree
breederPed <- qcStudbook(examplePedigree,
  minSireAge = 2L,
  minDamAge = 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)
#> The genetic value report 
#> Individuals in Pedigree: 327 
#> Male Founders: 3
#> Female Founders: 17
#> Total Founders: 20 
#> Founder Equivalents: 109.67 
#> Founder Genome Equivalents: 47.22 +/- 0.28 
#> Live Offspring: 321 
#> High Value Individuals: 240 
#> Low Value Individuals: 87 
summary(trimmedGeneticValue)
#> The genetic value report 
#> Individuals in Pedigree: 704 
#> Male Founders: 3
#> Female Founders: 17
#> Total Founders: 20 
#> Founder Equivalents: 116.8 
#> Founder Genome Equivalents: 65.90 +/- 0.19 
#> Live Offspring: 1004 
#> High Value Individuals: 285 
#> Low Value Individuals: 237