Select open pollinating plants

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)