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). Ideally I would also like to build in a variance structure to allow a different spread per land class. 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)) 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 noticed the discussion on the admb help forum entitled ?help with glmmADMB 0.6.4 - function maximizer failed? with Rafael Mares discusses similar problems. I have tried some of the suggested solutions, none of which have been recognised as code in R. I have also run:> summary(fm)Which results in: Error in summary(fm) : object 'fm' not found 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. Apologies for the long message! Many thanks, Emma Rosenfeld PhD student, School of Geography, Earth and Environmental Sciences, University of Birmingham -- View this message in context: http://r.789695.n4.nabble.com/help-with-glmmADMB-ZI-function-maximizer-failed-tp3918994p3918994.html Sent from the R help mailing list archive at Nabble.com.
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 foundWell, 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. >