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