Hello Amelie,
I don't have an answer to your question, but I just wanted to point out
this page I noticed recently (
http://hlplab.wordpress.com/2009/05/07/multinomial-random-effects-models-in-r/),
which might be helpful.
I'm also interested in figuring out how to do a multinomial glmm, so if you
find out anything I'd be happy to hear more about it! Based on what I've
found so far it seems like doing a multinomial glmm is not very
straightforward, unfortunately...
Best,
Steve Politzer-Ahles
Message: 94> Date: Wed, 12 Sep 2012 09:47:12 +0200
> From: Vaniscotte <vanamelie@gmail.com>
> To: r-help@r-project.org
> Subject: [R] multinomial MCMCglmm
> Message-ID: <50503E00.4060600@gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear all,
>
> I would like to add mixed effects in a multinomial model and I am trying
> to use MCMCglmm for that.
>
> The main problem I face: my data set consits of a trapping data set,
> where the observation at eah trap (1 or 0 for each species) have been
> aggregated per traplines. Therefore we have a proportion of
> presence/absence for each species per trapline.
>
> ex:
> ID_line mesh habitat Apsy Mygl Crle Crru Miag Miar Mimi Mumu Misu
> Soar Somi
> 11 028S6A 28 copse 2 0 0 0 0 0 0 0 0
> 0 0
> 12 028S6B 28 copse 1 1 0 0 0 0 0 0 0
> 0 0
> 13 028S6C 28 hedge 2 0 0 4 0 0 0 0 0
> 0 0
> 14 028S6D 28 hedge 1 0 0 7 0 0 0 0 1
> 0 0
> 15 028S6E 28 hedge 7 0 0 1 0 0 0 0 0
> 0 0
> empty
> 11 28
> 12 28
> 13 24
> 14 21
> 15 22
>
> When I run the following:
>
> > test1 <-
>
>
MCMCglmm(fixed=cbind(Apsy,Mygl,Crle,Crru,Miag,Miar,Mimi,Mumu,Misu,Soar,Somi,empty)~habitat,random=~mesh,family="multinomial12",data=metalSmA[,c(2,9,23:34)],rcov=~us(trait):units)
>
> I got some error when running regarding the variance structure:
>
> > "ill-conditioned G/R structure: use proper priors if you
haven't or
> rescale data if you have"
>
> I guess that the problem comes from the nature of my observation whih
> are frequencies rather than 0/1 per unit
>
> Does someone know if a multinomial model fitted with MCMCglmm can
> handdle those frequencies table and how to specify the good G/R variance
> structures?
>
>
> Regards
>
> Am?lie Vaniscotte
>
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