[R-sig-ME] 0-inflated GLMM in R

[Ben Bolker]

Katarzyna Kulma <katarzyna.kulma at ...> writes:

> 
> Hello ADMB-users!
 
> I'm new to glmmADMB and I just can't get it going. I'm trying to run
>  the model
 
> m1<-glmmadmb(rec~INFECTION*bin.age*ld+(1|RINGNO)+(1|year),
>  zeroInflation=TRUE,family="poisson")
> 
> where rec is a number of chicks recruited to the population a year
> after they fledged (heavily 0-inflated); INFECTION = a malaria
> infection status, 1=infected, 0=uninfected; bin.age=binomial age of
> parents (yearling, or older); ld-lay date, a covariate. The ring
> number and the year are random effects. Yet, when I run this model on  
> Mac OX 10.5.8 (R version 2.15) I receive a following message:
> 
> Error in parse(text = lab) : object 'lab' not found
> 
> In addition: Warning messages:
> 1: In is.na(rows) : is.na() applied to non-(list or vector) of type 'NULL'
> 2: In is.na(rows) : is.na() applied to non-(list or vector) of type 'NULL'
> 
> When I run it on Windows XP (R version 2.15), then I get this:
> 
> Error in II[, ii] = II[, ii] + REmat$codes[[i]] :
>    number of items to replace is not a multiple of replacement length
> In addition: Warning messages:
> 1: In glmmadmb(rec ~ INFECTION * bin.age * ld + (1 | RINGNO) + (1 |  :
>    NAs removed in constructing fixed-effect model frame: you should  
> probably remove them manually, e.g. with na.omit()
> 2: In II[, ii] + REmat$codes[[i]] :
>    longer object length is not a multiple of shorter object length
> 
> I receive these messages when I run the model in both, the most recent
> version of glmmADMB or the older one (0.7). Does anyone have any
> idea what is going on here? When I posted this question on ADMB-Users  
> mailing list, Dave Fourier suggested that it is probably an R issue  
> and encouraged me to post this message here. If there's no way I can  
> run ADMB, is there any other way I can run 0-inflated mixed models in  
> R? I'll appreciate any piece of advice

  I think the problem may be that you are not passing your data
to glmmADMB as a data frame.  This format is not supposed to
be required, but I haven't tested the alternative case (where
the variables are simply located in the global workspace) very
carefully, so there may be problems.

  Also note the error message on Windows, which tells you that
you should probably remove NA values from your data set before
proceeding.

  Can you give the results of sessionInfo() ?  Are you using version
0.7.2.12 from r-forge?