setPhenoProgTest {AlphaSimR}

Set progeny test as phenotype

Description

Models a progeny test of individuals in 'pop'. Returns 'pop' with a phenotype representing the average performance of their progeny. The phenotype is generated by mating individuals in 'pop' to randomly chosen individuals in testPop a number of times equal to 'nMatePerInd'.

Usage

setPhenoProgTest(
  pop,
  testPop,
  nMatePerInd = 1L,
  use = "pheno",
  h2 = NULL,
  H2 = NULL,
  varE = NULL,
  corE = NULL,
  reps = 1,
  fixEff = 1L,
  p = NULL,
  onlyPheno = FALSE,
  simParam = NULL
)

Arguments

pop

an object of Pop-class

testPop

an object of Pop-class

nMatePerInd

number of times an individual in 'pop' is mated to an individual in testPop

use

true genetic value (gv) or phenotypes (pheno, default)

h2

a vector of desired narrow-sense heritabilities for each trait. See details in setPheno.

H2

a vector of desired broad-sense heritabilities for each trait. See details in setPheno.

varE

error (co)variances for traits. See details in setPheno.

corE

an optional matrix for correlations between errors. See details in setPheno.

reps

number of replications for phenotype. See details in setPheno.

fixEff

fixed effect to assign to the population. Used by genomic selection models only.

p

the p-value for the environmental covariate used by GxE traits. If NULL, a value is sampled at random.

onlyPheno

should only the phenotype be returned, see return

simParam

an object of SimParam

Details

The reps parameter is for convenient representation of replicated data. It was intended for representation of replicated yield trials in plant breeding programs. In this case, varE is set to the plot error and reps is set to the number plots per entry. The resulting phenotype would reflect the mean of all replications.

Value

Returns an object of Pop-class or a matrix if onlyPheno=TRUE

Examples

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

#Set simulation parameters
SP = SimParam$new(founderPop)

SP$addTraitA(10)

#Create two populations of 5 individuals
pop1 = newPop(founderPop[1:5], simParam=SP)
pop2 = newPop(founderPop[6:10], simParam=SP)

#Set phenotype according to a progeny test
pop3 = setPhenoProgTest(pop1, pop2, use="gv", simParam=SP)