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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