[R-sig-ME] priors with MCMCglmm binomial analysis

[Eryn McFarlane]

Hi Massimo,

I'm not sure, but I was under the impression that binomial analysis in MCMCglmm should be done with the family ="categorical". I don't know if this will make a huge difference, but hopefully it helps!

Good Luck,

Eryn

Eryn McFarlane
MSc Candidate
Department of Integrative Biology
University of Guelph
Guelph, ON, Canada N1G 2W1

On 2011-12-07, at 11:14 AM, m.fenati at libero.it wrote:

> dear R users,
> I don't know how to set a MCMCglmm for binomial analysis. I'm trying to fit 
> several model but bad results were always observed if compared with the glm 
> results. 
> 
> My model is:
> 
> 
> tc<-matrix(c(124,184,33,18,86,9), ncol=2)
> 
> tco<-data.frame("specie"=c("bov","ov","cap"),"pos"= tc[,2],"tot"=tc[,1])
> 
> prior<-list(R=list(V=1,nu=0.002))
> 
> m.1<-MCMCglmm(cbind(pos,(tot-pos))~specie,prior=prior,data=tco,nitt=900000,
> thin=100,burnin=300000,family="multinomial2",verbose=FALSE)
> 
> 
> Large coefficient values and intervals occurred after fitting the model:
> 
>> summary(m.1)
> 
> Iterations = 300001:899901
> Thinning interval  = 100
> Sample size  = 6000 
> 
> DIC: 401.758 
> 
> R-structure:  ~units
> 
>      post.mean  l-95% CI  u-95% CI eff.samp
> units 594395401 0.0002638 1.418e+09     5106
> 
> Location effects: cbind(pos, (tot - pos)) ~ specie 
> 
>            post.mean  l-95% CI  u-95% CI eff.samp pMCMC
> (Intercept)     59.24 -20274.73  22702.05     6000 0.697
> speciecap      -62.28 -33022.96  28154.63     6000 0.815
> specieov      -142.82 -28811.83  30635.06     6000 0.717
> 
> 
> 
> When I fit a glm model, different and more reasonable results are observed:
> 
> m.1<-glm(cbind(pos,(tot-pos))~specie, data=tco, family="binomial")
> 
>> summary(m.1)
> 
> .........
> 
> Coefficients:
>            Estimate Std. Error z value Pr(>|z|)    
> (Intercept)  -1.7731     0.2549  -6.955 3.52e-12 ***
> speciecap     0.7922     0.4667   1.698   0.0896 .  
> specieov      1.6424     0.2947   5.574 2.49e-08 ***
> 
> 
> 
> Where is the error? a mistake in the model specification, priors setting, ... 
> I dont'know!
> I tried with other priors but the results never agree with the glm results.
> 
> 
> Could someone help me?
> 
> 
> Thanks in advance!
> 
> Regards
> 
> 
> 
> Massimo
> 
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