[R-sig-ME] priors for a multi-response model (MCMCglmm)

Ned Dochtermann ned.dochtermann at gmail.com
Mon Oct 11 22:06:25 CEST 2010

Hi all,

While I'm still struggling with properly specifying priors in general, I've
run into a specific problem I can't quite muddle through. I'm trying to
estimate the covariances among several behaviors with repeated measures per
individual. I initially did so using the following structure:

#I know this assumes unit variance

random=~us(trait):units, rcov=~us(trait):units,
family=c("poisson","poisson","poisson), data=Compiled, prior=multi.prior,

or if including fixed factors:
random=~us(trait):units, rcov=~us(trait):units,
family=c("poisson","poisson","poisson), data=Compiled, prior=multi.prior,

(I actually run both a lot longer than the defaults but I've left that out
here as it isn't relevant)

Both of these models seem to work well, they give reasonable answers and
satisfy a variety of diagnostics.

However, in looking back over the data I realized the data had pretty severe
zero-inflation. Thus, I've tried to rerun the analyses using zero-inflated
models. Based on the MCMCglmm course notes I thought that the first step for
the priors would be to expand both G and R to diag(4):

4)) #the last 'nu' is wrong based on how ZIP model priors are specified in
the course notes

random=~us(trait):units, rcov=~us(trait):units,

This doesn't work as "V is the wrong dimension for some priorG/priorR
elements". I also suspect it is more generally wrong due to the random and
rcov statements and issues with estimating aspects of the zero-inflation and
poisson covariances; however I'm specifically interested in estimating the
covariance matrix so I don't want to use an idh specification here.

I'd like to get the covariance matrix from a ZIP model but I'm not sure what
all the errors in the above coding are nor the solutions. Basically I know
both the specification of the prior and the specification of the model are
wrong. Any help would be greatly appreciated.


Ned Dochtermann
Department of Biology
University of Nevada, Reno

ned.dochtermann at gmail.com

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