sommer (version 3.1)

eig: eigen decomposition functionality

Description

This function allows mmer2 to detect when the user wants to perform an eigen decomposition of the additive relationship matrix in certain random effect.

Usage

eig(x)

Arguments

x

a column of a dataframe.

Value

$dd

an incidence matrix with columns for the specific levels specified.

References

Covarrubias-Pazaran G (2016) Genome assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11(6): doi:10.1371/journal.pone.0156744

See Also

The core functions of the package mmer and mmer2

Examples

# NOT RUN {
data(CPdata)
head(CPpheno)
CPgeno[1:4,1:4]
#### create the variance-covariance matrix 
A <- A.mat(CPgeno)
#### look at the data and fit the model
head(CPpheno)

mix1 <- mmer2(color~1,
              random=~ eig(g(id)), 
              rcov=~units,
              G=list(id=A), 
              data=CPpheno)
summary(mix1)

# mix2 <- mmer2(cbind(Yield,color)~1,
#               random=~ us(trait):eig(g(id)), 
#               rcov=~us(trait):units,
#               G=list(id=A), 
#               data=CPpheno)
# summary(mix2)

# }