[R-sig-ME] MCMCglmm ZIP longitudinal

[David Duffy]

On Sat, 27 Jul 2013, Thomas Houslay wrote:

> I have been struggling with some analysis for quite a long time now, and 
> hoping someone can help give me a little advice as to whether my current 
> model (using MCMCglmm) seems reasonable, in addition to answering a 
> question about autocorrelation in the zero-inflation term.
>
> The responses are counts of the time that an individual cricket spent 
> calling on the day of measurement (each individual is measured at weekly 
> intervals from 1 week after reaching adulthood until death), and appear 
> to be highly overdispersed compared to standard Poisson, and also 
> zero-inflated – I have therefore been using the ZIP model in MCMCglmm.
[...]
> Each individual was raised on one of two diet 
> treatments during the nymph stage (ie, before measurements started), and 
> then assigned to one of two diet treatments again at adulthood. I am 
> interested in the effect of diet and age (and their interactions) on the 
> pattern of calling.

I have spent some time resisting the urge to respond to this :), since I 
can make only really general remarks. The question about mixing is really 
hard - I see these models and methods as still experimental.  The 
proposals for the MCMC may be exploring the whole space really slowly 
because the parameterization is not optimal for that particular problem, 
or it can just be stuck. There are no foolproof diagnostics, so experts 
still spend a lot of time staring at plots, and simulating data from 
the proposed model and seeing if they then can recapture the right answer.

And I have great difficulty understanding what you will do with all these 
interaction terms.  If you can't get rid of them my first thought would be 
to maybe try a "straightforward" non-linear or semiparametric (GAMMs etc) 
model for individual trajectory, and look for treatment effects on 
velocity or higher order terms.

Just 1.5c, David.

| David Duffy (MBBS PhD)                                         ,-_|\
| email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v