AlphaSimR (version 0.10.0)

genParam: Sumarize genetic parameters

Description

Calculates genetic and genic additive and dominance variances for an object of Pop-class

Usage

genParam(pop, simParam = NULL)

Arguments

pop

an object of Pop-class

simParam

an object of SimParam

Value

varA

an nTrait by nTrait matrix of additive genetic variances

varD

an nTrait by nTrait matrix of dominance genetic variances

varAA

an nTrait by nTrait matrix of additive-by-additive genetic variances

varG

an nTrait by nTrait matrix of total genetic variances

genicVarA

an nTrait vector of additive genic variances

genicVarD

an nTrait vector of dominance genic variances

genicVarAA

an nTrait vector of additive-by-additive genic variances

genicVarG

an nTrait vector of total genic variances

randGenicVarA

an nTrait vector of additive genic variances assuming random mating

randGenicVarD

an nTrait vector of dominance genic variances assuming random mating

randGenicVarAA

an nTrait vector of additive-by-additive genic variances assuming random mating

randGenicVarG

an nTrait vector of total genic variances assuming random mating

mu

an nTrait vector of trait means

mu_HWE

an nTrait vector of expected trait means under Hardy-Weinberg equilibrium

gv

a matrix of genetic values with dimensions nInd by nTraits

bv

a matrix of breeding values with dimensions nInd by nTraits

dd

a matrix of dominance deviations with dimensions nInd by nTraits

aa

a matrix of additive-by-additive deviations with dimensions nInd by nTraits

gv_mu

an nTrait vector of trait means for genotype with all zeros

gv_a

a matrix of additive genetic values with dimensions nInd by nTraits

gv_d

a matrix of dominance genetic values with dimensions nInd by nTraits

gv_aa

a matrix of additive-by-additive genetic values with dimensions nInd by nTraits

Examples

# NOT RUN {
#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitAD(10, meanDD=0.5)
SP$setVarE(h2=0.5)

#Create population
pop = newPop(founderPop, simParam=SP)
ans = genParam(pop, simParam=SP)

# }