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The examples below illustrate how to fit models for binary and ordinal traits using BGLR.
Binary
library(BGLR)
data(wheat)
y=wheat.Y[,1]
X=scale(wheat.X)
yBin<-ifelse(y>quantile(y,prob=.66),1,0)
fm=BGLR(yBin,response_type='ordinal',ETA=list(list(X=X,model='BRR')),nIter=6000,burnIn=1000)
fm$varE # fixed to 1 for identification
fm$mu # same as above
fm$threshold
head(fm$probs)
boxplot(fm$probs[,2]~yBin)
Ordinal
yOrdinal=ifelse(y<quantile(y,prob=.33),1,ifelse(y<quantile(y,prob=.66),2,3))
table(yOrdinal)
fm=BGLR(yOrdinal,response_type='ordinal',ETA=list(list(X=X,model='BRR')),nIter=6000,burnIn=1000)
fm$varE # fixed to 1 for identification
fm$mu # same as above
fm$threshold
head(fm$probs)
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