[R-sig-ME] zero-inflated models in MCMCglmm

Gustaf Granath gustaf.granath at gmail.com
Fri Nov 25 14:16:30 CET 2016

A few questions regarding zero-inflated models using MCMCglmm.

1. Odd contrasts are created when using, e.g. :
y ~ trait-1 + at.level(trait, 1):(X1+X2), family = "zipoisson" #X1 and 
X2 are factors with 2 levels
at.level(trait, 1):X1lev1
at.level(trait, 1):X1lev2
at.level(trait, 1):X2lev2

It doesnt look like this in the course notes (what I can see). Is 
at.level(trait, 1):X1lev1 the reference level for everything below? I 
also get very high (>1000) estimates for traity, at.level(trait, 
1):X1lev1 and at.level(trait, 1):X1lev2.

2. I made four models
a) y ~ X1*X2, family = "poisson"
Large overdispersion (units ~ 5) but everything looks fine (traceplots, 
random effects (including units) ). Predictive checks show that the 
models predict too few zeros though. And alarming is that predictions 
are really bad, e.g. a treatment mean of 40 is predicted to have 300 counts.

b) y ~ trait-1 + at.level(trait, 1):(X1+X2), family = "zipoisson"
Model looks OK, but again, predictions are way too high for the higher 
tretament means.

c:d) y ~ trait-1 + at.level(trait, 1):(X1+X2), family = "zapoisson" or 
Predicted values are much better. But is it the same way get predictions 
here? Possible to get predictions from the separate models 
(poisson/binomial) in the hurdle case? (code available?)
#get e.g. treatment predictions?
predict.MCMCglmm(model, marginal = ~ random_factor, type="response", 
posterior = "mean")

The "zapoisson" model performs best but I dont understand why the 
"zipoisson" is so bad. Any typical things to look for when it looks like 
Interpreting "zapoisson" isnt easy, any good literature/tutorials on 
this model?




Gustaf Granath
Post doc
Swedish University of Agricultural Sciences

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