help with glmmADMB ZI; function maximizer failed
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.