nprcgenekeepr (version 2.0.0)

makeSimPed: Make a simulated pedigree from representative sires and dams

Description

For each id in allSimParents, an unknown (NA) sire or dam is imputed by a random draw from the supplied representative vectors (sires and dams); a known sire or dam is preserved unchanged. When a parent is unknown and its representative vector is empty, that parent remains NA.

Usage

makeSimPed(ped, allSimParents, verbose = FALSE)

Value

simulated pedigree in data.frame format with the id, sire, and dam.

Arguments

ped

The pedigree information in data.frame format

allSimParents

list made up of lists where the internal list has the offspring ID id, a vector of representative sires (sires), and a vector of representative dams (dams).

verbose

logical vector of length one that indicates whether or not to print out when an animal is missing a sire or a dam.

Details

The algorithm assigns parents randomly from the lists of possible sires and dams and does not prevent a dam from being selected more than once within the same breeding period. While this is probably not introducing a large error, it is not ideal.

Examples

library(nprcgenekeepr)
ped <- nprcgenekeepr::lacy1989Ped
## For each id below, any unknown sire/dam is replaced by a random
## draw from the supplied representative sires and dams.
allSimParents <- list(
  list(
    id = "A",
    sires = c("s1_1", "s1_2", "s1_3"),
    dams = c("d1_1", "d1_2", "d1_3", "d1_4")
  ),
  list(
    id = "B",
    sires = c("s2_1", "s2_2", "s2_3"),
    dams = c("d2_1", "d2_2", "d2_3", "d2_4")
  ),
  list(
    id = "E",
    sires = c("s3_1", "s3_2", "s3_3"),
    dams = c("d3_1", "d3_2", "d3_3", "d3_4")
  )
)
set.seed(1)
simPed <- makeSimPed(ped, allSimParents)
simPed