selectOP: Select open pollinating plants

In AlphaSimR: Breeding Program Simulations

Select open pollinating plants

Description

This function models selection in an open pollinating plant population. It allows for varying the percentage of selfing. The function also provides an option for modeling selection as occuring before or after pollination.

Usage

selectOP(
  pop,
  nInd,
  nSeeds,
  probSelf = 0,
  pollenControl = FALSE,
  trait = 1,
  use = "pheno",
  selectTop = TRUE,
  candidates = NULL,
  simParam = NULL,
  ...
)

Arguments

pop	and object of Pop-class or MultiPop-class
nInd	the number of plants to select
nSeeds	number of seeds per plant
probSelf	percentage of seeds expected from selfing. Value ranges from 0 to 1.
pollenControl	are plants selected before pollination
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.
selectTop	selects highest values if true. Selects lowest values if false.
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 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 new population by selecting the best 3 plant
#Assuming 50% selfing in plants and 10 seeds per plant
pop2 = selectOP(pop, nInd=3, nSeeds=10, probSelf=0.5, simParam=SP)

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