simulatePed: Simulate pedigree, genetic merits and phenotypes

In pedSimulate: Pedigree, Genetic Merit, Phenotype, and Genotype Simulation

Simulate pedigree, genetic merits and phenotypes

Description

Simulate pedigree, genetic merits and phenotypes with random/assortative/disassortative matings followed by random/non-random selection of males and females with similar/different selection patterns in males and females.

Usage

simulatePed(
  F0size,
  Va0,
  Ve,
  littersize = 1,
  ngen,
  mort.rate = 0,
  overlap.s = 0,
  overlap.d = 0,
  f.rate = 1,
  m.rate = 1,
  fsel = "R",
  msel = "R",
  f.order = "fsel",
  m.order = "msel",
  seed = NA
)

Arguments

F0size	: Even number of founder animals. No mortality, selection and non-random mating in this generation.
Va0	: Additive genetic variance in the base generation (i.e., F0).
Ve	: Residual variance, constant across generations.
littersize	: Litter size, default = 1.
ngen	: Number of generations to simulate after the founder generation.
mort.rate	: Mortality rate per generation, after the availability of phenotype (e.g., birth weight, weaning weight) and before the age of maturity (i.e., before mating), default = 0. Maximum mort.rate = 0.5.
overlap.s	: Number of overlapping generations for sires, default = 0 for no generation overlap.
overlap.d	: Number of overlapping generations for dams, default = 0 for no generation overlap.
f.rate	: Proportion of females selected as dams, default = 1.
m.rate	: Proportion of males (<= f.rate) selected as sires, default = 1.
fsel	: If "R" (default), random selection on females; if "P", selection on phenotypes or true breeding values if Ve = 0; if "PA", selection on true parent averages. "-P" and "-PA" work in opposite direction of "P" and "PA", respectively.
msel	: If "R" (default), random selection on males; if "P", selection on phenotypes or true breeding values if Ve = 0; if "PA", selection on true parent averages. "-P" and "-PA" work in opposite direction of "P" and "PA", respectively.
f.order	: Ordering selected females for mating; if "fsel" (default), same as the selection order; if "R" random ordering; if "P", ordering based on phenotypes or true breeding values if Ve = 0; if "PA", ordering based on true parent averages. "-P" and "-PA" work in opposite direction of "P" and "PA", respectively.
m.order	: Ordering selected males for mating; if "msel" (default), same as the selection order; if "R" random ordering; if "P", ordering based on phenotypes or true breeding values if Ve = 0; if "PA", ordering based on true parent averages. "-P" and "-PA" work in opposite direction of "P" and "PA", respectively.
seed	: A numeric variable input to the random number generator for reproducible simulations, default = 'NA' for non-reproducible simulations.

Details

The output pedigree data.frame (ped) has 9 columns: ID, SIRE, DAM, SEX, GEN (generation number starting with 0 for the base generation), PA (parent average), MS (Mendelian Sampling), E (environment and residuals), and P (phenotype).

Random, assortative, and disassortative matings can be simulated with different combinations of fsel, msel, f.order, and m.order.

Value

ped : The output pedigree data.frame. Further information provided in Details.

Examples

ped = simulatePed(
    F0size = 100,
    Va0 = 9,
    Ve = 36,
    littersize = 2,
    ngen = 4,
    mort.rate = 0.05,
    overlap.s = 1,
    overlap.d = 0,
    f.rate = 0.8,
    m.rate = 0.5,
    fsel = "P",
    msel = "PA",
    f.order = "fsel",
    m.order = "msel",
    seed = 68
)

pedSimulate documentation built on Sept. 26, 2023, 9:06 a.m.