Calculates genetic and genic additive and dominance variances
for an object of Pop-class
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
- covA_HW
an nTrait vector of additive covariances due to non-random mating
- covD_HW
an nTrait vector of dominance covariances due to non-random mating
- covAA_HW
an nTrait vector of additive-by-additive covariances due to non-random mating
- covG_HW
an nTrait vector of total genic covariances due to non-random mating
- covA_L
an nTrait vector of additive covariances due to linkage disequilibrium
- covD_L
an nTrait vector of dominance covariances due to linkage disequilibrium
- covAA_L
an nTrait vector of additive-by-additive covariances due to linkage disequilibrium
- covAD_L
an nTrait vector of additive by dominance covariances due to linkage disequilibrium
- covAAA_L
an nTrait vector of additive by additive-by-additive covariances due to linkage disequilibrium
- covDAA_L
an nTrait vector of dominance by additive-by-additive covariances due to linkage disequilibrium
- covG_L
an nTrait vector of total genic covariances due to linkage disequilibrium
- mu
an nTrait vector of trait means
- mu_HW
an nTrait vector of expected trait means under random mating
- 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 epistatic deviations with dimensions nInd by nTraits
- gv_mu
an nTrait vector of intercepts with dimensions nInd by nTraits
- 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
- alpha
a list of average allele subsitution effects with length nTraits
- alpha_HW
a list of average allele subsitution effects at Hardy-Weinberg equilibrium with length nTraits
Examples
#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)