selectWithinFam: Select individuals within families

In AlphaSimR: Breeding Program Simulations

Select individuals within families

Description

Selects a subset of nInd individuals from each full-sib family within a population. Will return all individuals from a full-sib family if it has less than or equal to nInd individuals.

Usage

selectWithinFam(
  pop,
  nInd,
  trait = 1,
  use = "pheno",
  sex = "B",
  famType = "B",
  selectTop = TRUE,
  returnPop = TRUE,
  candidates = NULL,
  simParam = NULL,
  ...
)

Arguments

pop	and object of Pop-class, HybridPop-class or MultiPop-class
nInd	the number of individuals to select within a family
trait	the trait for selection. Either a number indicating a single trait or a function returning a vector of length nInd. The function must work on a vector or matrix of use values as trait(pop@use, ...) - depending on what use is. See the examples and selIndex.
use	the selection criterion. Either a character (genetic values "gv", estimated breeding values "ebv", breeding values "bv", phenotypes "pheno", or randomly "rand") or a function returning a vector of length nInd. The function must work on pop as use(pop, trait, ...) or as trait(pop@use, ...) depending on what trait is. See the examples.
sex	which sex to select. Use "B" for both, "F" for females and "M" for males. If the simulation is not using sexes, the argument is ignored.
famType	which type of family to select. Use "B" for full-sib families, "F" for half-sib families on female side and "M" for half-sib families on the male side.
selectTop	selects highest values if true. Selects lowest values if false.
returnPop	should results be returned as a Pop-class. If FALSE, only the index of selected individuals is returned.
candidates	an optional vector of eligible selection candidates.
simParam	an object of SimParam
...	additional arguments if using a function for trait and use

Value

Returns an object of Pop-class, HybridPop-class or MultiPop-class

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)

SP$addTraitA(10)
SP$setVarE(h2=0.5)

#Create population
pop = newPop(founderPop, simParam=SP)

#Create 3 biparental families with 10 progeny
pop2 = randCross(pop, nCrosses=3, nProgeny=10, simParam=SP)

#Select best individual per family
pop3 = selectWithinFam(pop2, 1, simParam=SP)

AlphaSimR documentation built on Nov. 1, 2024, 5:07 p.m.