Tabulate offspring counts, optionally by population — offspringCounts • nprcgenekeepr

Optionally find the number that are part of the population of interest.

Usage

offspringCounts(probands, ped, considerPop = FALSE)

Arguments

probands: character vector of egos for which offspring should be counted.
ped: the pedigree information in datatable format. Pedigree (req. fields: id, sire, dam; population is also read when considerPop is TRUE). This is the complete pedigree.
considerPop: logical value indication whether or not the number of offspring that are part of the focal population are to be counted? Default is FALSE. If ped has no population column, considerPop has no effect and only totalOffspring is returned.

Value

A dataframe containing the column totalOffspring (and livingOffspring when considerPop is TRUE and ped has a population column). The animal ids are the data frame row names when probands are unique; duplicated probands give sequential row names.

Examples

library(nprcgenekeepr)
examplePedigree <- nprcgenekeepr::examplePedigree
breederPed <- qcStudbook(examplePedigree,
  minSireAge = 2,
  minDamAge = 2,
  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]
counts <- offspringCounts(probands, ped)