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
orMultiPop-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. See the examples inselectInd
andselIndex
.- 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.
- candidates
an optional vector of eligible selection candidates.
- simParam
an object of
SimParam
- ...
additional arguments if using a function for trait
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 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)