Nothing
rm(list=ls())
library(BLR)
data(wheat) #Loads the wheat dataset
y=Y[,1]
### Creates a testing set with 100 observations
whichNa<-sample(1:length(y),size=100,replace=FALSE)
yNa<-y
yNa[whichNa]<-NA
### Runs the Gibbs sampler
fm<-BLR(y=yNa,XL=X,GF=list(ID=1:nrow(A),A=A),
prior=list(varE=list(df=3,S=0.25),
varU=list(df=3,S=0.63),
lambda=list(shape=0.52,rate=1e-4,
type='random',value=30)),
nIter=5500,burnIn=500,thin=1,
saveAt="example_")
MSE.tst<-mean((fm$yHat[whichNa]-y[whichNa])^2)
MSE.tst
MSE.trn<-mean((fm$yHat[-whichNa]-y[-whichNa])^2)
MSE.trn
COR.tst<-cor(fm$yHat[whichNa],y[whichNa])
COR.tst
COR.trn<-cor(fm$yHat[-whichNa],y[-whichNa])
COR.trn
plot(fm$yHat~y,xlab="Phenotype",
ylab="Pred. Gen. Value" ,cex=.8)
points(x=y[whichNa],y=fm$yHat[whichNa],col=2,cex=.8,pch=19)
x11()
plot(scan('example_varE.dat'),type="o",
ylab=expression(paste(sigma[epsilon]^2)))
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