Anova/deviance table in glmmADMB

Le 20/03/2012 22:43, Ben Bolker a ?crit : On 12-03-20 02:32 PM,
Thomas Merkling wrote:

Dear Ben and other list members,

- Is there any way to produce a Anova/deviance table for a
model fitted with glmmADMB ? I used the Anova() function from
the car library for glmer models, but it does not seem to
work with glmmadmb (I'm using glmmADMB 0.7) and I would like
only one p-value for each term and interaction and NOT one
p-value for each level of the interaction.

Hmmm.

car::Anova() should work now -- I had to add a model.frame() and a 
df.residual() method for glmmadmb objects.  (The df.residual
number may be a little dodgy -- I'm not sure I counted the
parameters right -- but I don't think it's actually used for much
by default, cause you get Wald chi-square tests)

The newest version of glmmADMB is 0.7.5.1 -- it may take a little 
while for r-forge to catch up, and I was having a few dependency 
issues.  If you don't see it there in ~ 24 hours, drop me a line.

I used glmmADMB 0.7 because some models did not converge with
glmmADMB 0.7.2.4 ("function maximizer failed (couldn't find the
STD file)")  and I read that with it might work with previous
versions ... which was the case .. until today .... Models that
were fitted without problem yesterday did not convernge today:
"Memory allocation error -- Perhaps you are trying to allocate 
too much memory in your program"  and  "function maximizer
failed (couldn't find the STD file)"

I was never able to download the package via

install.packages("glmmADMB", 
repos="http://r-forge.r-project.org",type="source")

I got a warning :

In getDependencies(pkgs, dependencies, available, lib) : package
'glmmADMB' is not available (for R version 2.14.2)

And on theR-forge packages page for the glmmADMB project 
<https://r-forge.r-project.org/R/?group_id=847>  the build status
is "Failed to build" and I never found any source package, but
maybe I was not looking at the right place ...

I will have a look tomorrow if things have changed ...

- I also tried to compare nested models via LRT using 
anova(model1,model2) for glmmADMB models but I didn't get
any p-values, it produced NaN, although it apparently
calculate the differences in likelihood. Where can this come
from ?

This ought to have worked: perhaps you had the models in the wrong 
order?

I think I did it right .... Here is an example

modmean=glmmadmb(MeanAggr~Date + Age+ Obs+ 
(1|Nest),family="Gamma",data=YESaggr,verbose=FALSE) modmean1=
glmmadmb(MeanAggr~Date + Age+ 
(1|Nest),family="Gamma",data=YESaggr,verbose=FALSE)

anova(modmean,modmean1) Analysis of Variance Table

Model 1: MeanAggr ~ Date + Age + Obs Model 2: MeanAggr ~ Date +
Age NoPar  LogLik Df  -2logQ P.value 1     9 -726.22 2     5
-731.23 -4 -10.012 Message d'avis : In pchisq(q, df, lower.tail,
log.p) : production de NaN

If is specify "test="Chisq"", I got this error message : Erreur
dans x$random : $ operator is invalid for atomic vectors

- I tried to use the coefplot2 library (downloaded from 
http://www.math.mcmaster.ca/bolker/R/src/contrib) as showed
on the glmmADMB home page ("getting started with glmmADMB"),
but I couldn't use it and got this error message : unable to
find an inherited method for function "coefplot2", for
signature "glmmadmb". Is it normal ? It worked fine with
glmer output.

Can you try getting it from r-forge?

Again, if the problem persists let me know.

Ben

on theR-forge packages page for the coefplot2 project 
<https://r-forge.r-project.org/R/?group_id=847>  the build status
is offline and I got the same error message as for glmmADMB when
trying

install.packages("coefplot2", 
repos="http://r-forge.r-project.org",type="source")

Cheers, Thomas

Thanks for your help ! Thomas