AlphaSimR (version 1.6.0)

selectFam: Select families

Description

Selects a subset of full-sib families from a population.

Usage

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

Value

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

Arguments

pop

and object of Pop-class, HybridPop-class or MultiPop-class

nFam

the number of families to select

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

Examples

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

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$nThreads = 1L
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 2 families
pop3 = selectFam(pop2, 2, simParam=SP)