[R-sig-ME] Multivariate multinomial in MCMCglmm

[Jarrod Hadfield]

Hi Szymek,

cbind(response1, response2)~trait ...

If we use the notation A.B to denote log odds ratios for category A in  
response B, then the traits in order are 2.1, 3.1, 2.2, 3.2, 4.2. You  
can use things like at.level(trait, 1:2) and at.level(trait, 3:5) if  
you only want to fit effects for one of the responses.

Note that the prior G1=list(V=IJ, nu=K-1+0.002))  is likely to have a  
large effect.

Cheers,

Jarrod


Quoting Szymek Drobniak <szymonmarian.drobniak at uzh.ch> on Wed, 13 Aug  
2014 18:03:15 +0200:

> Dear List Members,
>
> I'm wondering if you have experience (if it's passible in the first place)
> in fitting a mixed model with multiple multinomial responses in MCMCglmm. I
> was trying to fit such model but I bumped into the truble of what the
> "trait" dummy variable does actually index in such a model?
>
> In a "univariate" multinomial model (which actually already is
> multivariate) like the one below the trait variable indexes single odds
> ratios for 2nd/3rd... category against the 1st category. Is it possible to
> extend this into a situation with more than one multinomial variables?
>
>
> cheers,
> Szymek
>
> require(MCMCglmm)
>
> mydata <- data.frame(response1 = c(sample(c("a","b","c"), replace=T, size =
> 100)),
>                      covariate = rnorm(100), random =
> gl(20,5,labels=letters[1:20]))
>
>
> K <- length(levels(mydata$response1))
> I <- diag(K-1)
> J <- matrix(0,K-1,K-1) + 1
> IJ <- 1/K*(I+J)
>
> size=2
> prior <- list(R=list(V=IJ, fix=1),
>               G=list(G1=list(V=IJ, nu=K-1+0.002)),
>               B=list(mu=rep(0,size*(K-1)), V=kronecker(IJ,
> diag(size))*(1.7+pi^2/3)))
>
> model <- MCMCglmm(response1~trait*covariate-1, random=~us(trait):random,
> rcov=~us(trait):units,
>                   family="categorical", data=mydata, prior=prior)
>
> #######################################
>
> ## now what to do with the 2nd response variable?
>
> mydata$response2 <- as.factor(c(sample(c("w","x","y","z"), replace=T, size
> = 100)))
>
>
> --
>
> *Dr Szymon Drobniak*
> Anthropological Institute and Museum
> Office Y42-K-66
> University of Zürich - Irchel
> Winterthurerstrasse 190
> CH-8057 Zürich, Switzerland
>
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>
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