[R] help with glmmADMB ZI; function maximizer failed

[Ben Bolker]

emmarosenfeld <emmarosenfeld <at> hotmail.co.uk> writes:

> 
> Dear all,
> 
> I am having some problems trying to run a GLMM model with zero-inflation
> using the alpha version of glmmADMB (0.6.4) using R (2.13.1) in Windows and
> I would greatly appreciate some help. 
> My count response variable (number of birds: count) fits a negative binomial
> distribution and the explanatory variables are both continuous and
> categorical (species= 17). The three random effects are site (68 of them),
> season (1 or 2) and land class (1 to 6). 

  You mean species is a factor with 17 levels?

  What are the results of str(srp12) ?
 
  You are going to have a lot of difficulty fitting a random effect
to a factor with two levels (see http://glmm.wikidot.com/faq for
discussion).  Try it as a fixed effect instead.

> Ideally I would also like to build
> in a variance structure to allow a different spread per land class.

  I don't know of a way to do this in glmmADMB. **Maybe** doable
in MCMCglmm but I wouldn't count on it.

> This is
> the model I'm trying to run: 
> (fm<-glmmadmb(count~species*btrees+species*built+species*btrees*built+
 (1|season)+(1|landclass)+(1|site),
   data=srp12, famil="nbinom", zeroInflation=TRUE))

  Are you aware that species*btrees*built expands to include
all main effects, two- and three-way interactions, i.e. the
species*btrees and species*built terms are redundant.

> I have read most of the supporting documents to glmmADMB and studied the
> examples but am still struggling to make headway.
> 
> This is the error message I get; 
> 
> Memory allocation error -- Perhaps you are trying to allocate too much
> memory in your program 
> Warning: running command 'C:\Windows\system32\cmd.exe /c
> "C:/R-2.13.1/library/glmmADMB/bin/windows32/glmmadmb.exe" -maxfn 500' had
> status 1
> Warning in shell(cmd, invisible = TRUE) :
>   '"C:/R-2.13.1/library/glmmADMB/bin/windows32/glmmadmb.exe" -maxfn 500'
> execution failed with error code 1
> Error in glmmadmb(count ~ species * btrees + species * built + species *  : 
>   The function maximizer failed

    
> 
> I have also run: 
> 
> > summary(fm)
> 
> Which results in:
> 
> Error in summary(fm) : object 'fm' not found

  Well, that's not surprising since the command failed.
> 
> This has happened however the equation is labelled.
> 
> Perhaps there is a more appropriate package that I should be using
> (MCMCglmm)?
> I am quite new to R, so it is quite possible that I am missing something, so
> any help would be most appreciated.
>