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

[Mikhail Matz]

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