The following example illsutrates how to fit models with heterogeneous variances in BGLR. The same option can be used with any of the models fitted by BGLR, except RKHS.
varGroups=sample(1:3,size=1000,replace=T)
VAR=c(.1,.5,1)
error=rnorm(sd=sqrt(VAR)[varGroups],n=length(varGroups))
fm=BGLR(y=error, groups=varGroups)
cbind(VAR,fm$varE)
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