[R-sig-ME] MCMCglmm poisson / not poisson

[Jarrod Hadfield]

Hi,

If you calculate latentsv (a vector of variances from the posterior  
distribution of the residuals), and replace

exp(latents[i])

with

exp(latents[i]+0.5*latentsv[i])

does this improve things?

Cheers,

Jarrod

Quoting Mikhail Matz <matz at utexas.edu> on Tue, 28 Aug 2012 22:06:45 -0500:

>
> Hello -
>
> I am playing with ways to justify that the MCMCglmm model fits my  
> data well, which is quite important for me since I am hoping to be  
> able to suggest MCMCglmm-based modeling as a general solution for a  
> particular type of analysis.
>
> I am running "poisson" family on counts data, with two random  
> effects. Following Elston, D. A., R. Moss, et al. (2001).  
> Parasitology 122: 563-569., I am checking whether my lognormal  
> residuals (latent variable minus predicted value) are normally  
> distributed (check), if my random effects (saved with pr=T) are  
> normally distributed (more or less check), and then I try to see if  
> the observed counts really look like Poisson samples based on the  
> latent variables. Again, following Elston et al, I am making a p-p  
> plot using this script (expert coders, please don't judge):
>
> pp.poisson=function(counts,latents) {
> 	sim=c()
> 	for(i in 1:length(counts)){
> 		if (is.na(counts[i])) next
> 		data=counts[i]
> 		low=ppois(data,exp(latents[i]))-dpois(data,exp(latents[i]))
> 		up=ppois(data,exp(latents[i]))
> 		ss=seq(low,up,(up-low)/100)
> 		sim=append(sim,sample(ss,1))
> 	}
> 	sims=sort(sim)
> 	xx=(rank(sims)-0.5)/length(sims)
> 	plot(sims~xx)
> 	abline(0,1)
> }
>
> … and unfortunately it looks really ugly, like a very strongly bent   
> ' ~ ' rather than a line.
> The little script above seems to work; here is a sanity check:
>
> psim=c()
> nnn=rnorm(500,10,10)
> for (i in 1:length(nnn)){
> 	psim=append(psim,rpois(1,exp(nnn[i])))
> }
> pp.poisson(psim,nnn)
>
> I will be extremely grateful for any comments on this.
>
> cheers
>
> Misha
> UT Austin
>
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>



-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.