MCMCglmm and prior specification
Dear all, I am trying to use the MCMCglmm package to create credibility intervals for random variables in my data. I'm having a bit of trouble though determining what the best prior to use for each model is, since the results seem to differ tremendously depending on which prior I am using, for instance, I've tried these three types of priors,
halfFam<-var(data$Family)/2 prior1=list(R=list(V=1,n=1,fix=1),G=list(G1=list(V=1,n=1),G2=list(V=1,n=1))) prior2=list(R=list(V=1,n=1),G=list(G1=list(V=1,n=1),G2=list(V=1,n=1))) prior3=list(R=list(V=halfFam,n=1),G=list(G1=list(V=halfFam,n=1),G2=list(V=halfFam,n=1)))
For the model,
model<-MCMCglmm(Length~1,random=~Family+Rep,data=data,verbose=FALSE,prior=prior,burnin=10000,nitt=75000)
Where the random factors are Family and Replicate. From these priors, I get intervals for my Family effect,
HPDinterval(model1$VCV[,"Family"])
lower upper var1 0.09660338 0.8888039
HPDinterval(model2$VCV[,"Family"])
lower upper var1 0.1944570 2.120540
HPDinterval(model3$VCV[,"Family"])
lower upper var1 0.2099238 1.529794 I feel bad that I don't understand better how to specify the components of these priors, but from what I understand, the model should return similar values even if the priors are very different. I've looked through the vignette thoroughly, but didn't get a sense of what I was supposed to do if alternate priors returned different answers. I'm not sure whether this is telling me that all the information is coming from my priors (and there is, in fact, no information in the data), or I am just incorrectly specifying my priors. Any insight would be very much appreciated! Happy holidays, Cristina Ledon-Rettig UNC-Chapel Hill *I am using lme4 version 0.99375-28 with Mac OS X version 10.5