selectCross: Select and randomly cross

In AlphaSimR: Breeding Program Simulations

Select and randomly cross

Description

This is a wrapper that combines the functionalities of randCross and selectInd. The purpose of this wrapper is to combine both selection and crossing in one function call that minimized the amount of intermediate populations created. This reduces RAM usage and simplifies code writing. Note that this wrapper does not provide the full functionality of either function.

Usage

selectCross(
  pop,
  nInd = NULL,
  nFemale = NULL,
  nMale = NULL,
  nCrosses,
  nProgeny = 1,
  trait = 1,
  use = "pheno",
  selectTop = TRUE,
  simParam = NULL,
  ...,
  balance = TRUE
)

Arguments

pop	an object of Pop-class
nInd	the number of individuals to select. These individuals are selected without regards to sex and it supercedes values for nFemale and nMale. Thus if the simulation uses sexes, it is likely better to leave this value as NULL and use nFemale and nMale instead.
nFemale	the number of females to select. This value is ignored if nInd is set.
nMale	the number of males to select. This value is ignored if nInd is set.
nCrosses	total number of crosses to make
nProgeny	number of progeny per cross
trait	the trait for selection. Either a number indicating a single trait or a function returning a vector of length nInd.
use	select on genetic values "gv", estimated breeding values "ebv", breeding values "bv", phenotypes "pheno", or randomly "rand"
selectTop	selects highest values if true. Selects lowest values if false.
simParam	an object of SimParam
...	additional arguments if using a function for trait
balance	if using sexes, this option will balance the number of progeny per parent. This argument occurs after ..., so the argument name must be matched exactly.

Value

Returns an object of Pop-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)

#Select 4 individuals and make 8 crosses
pop2 = selectCross(pop, nInd=4, nCrosses=8, simParam=SP)

AlphaSimR documentation built on Nov. 2, 2023, 6:01 p.m.