[ADMB Users] gradient_structure problem with nbinom glmm.admb in R

[Rafael Mares]

Hi Mollie

Thanks for the quick reply. I'm trying to run an intercept only model
with individual identity (group="id") and group identity
(random=~group) as random effects. I have 230 individuals and 15
groups (14 - 200 individuals per group, and 1 - 60 measures per
individual). I usually use lme4, where I would have individuals nested
in groups (as individuals are unique to groups), but I am aware that
this isn't possible with glmmADMB (or at least not obvious), so I am
just trying to specify them as two separate random effects (two
sources of variation for the intercept)... hopefully this makes sense.
Maybe I'm not specifying this correctly in the model - I'm not yet too
familiar with the notation in glmm.admb

I can run the model with ' random=~1, group="id" ' with no problem,
but that leaves my group identities out of the picture. Any
suggestions?

Thanks again for your help and interest.

Raff

--
Rafael Mares
Large Animal Research Group (LARG)
Department of Zoology
University of Cambridge
Downing Street
Cambridge
CB2 3EJ



On 12 June 2011 12:23, Mollie Brooks <mbrooks at ufl.edu> wrote:
> Hi Rafael,
> You might be miss-specifying your model.
> You may want
>
> mix<-glmm.admb(dur~1,random=~1,group="id",data=dat,family="nbinom",easyFlag=FALSE,verbose=TRUE)
>
> This would make an intercept only model but allow the different levels
> of "id" to vary in their intercept. Depending on your experimental design,
> this might be what you want. What relationship were you hoping the model to
> represent?
> cheers,
> Mollie
> Mollie Brooks
> Ph.D. Candidate
> NSF IGERT Fellow
> Biology Department
> University of Florida
> mbrooks at ufl.edu
> www.zoology.ufl.edu/mbrooks
>
>
> On 12 Jun 2011, at 7:04 AM, Rafael Mares wrote:
>
> Dear all
>
> I am trying to run the following model using glmmADMB (ver. 0.5-2) in
> R (ver. 2.13.0) in a linux terminal:
>
> rmix<-glmm.admb(dur~1,random=~group,group="id",data=dat,family="nbinom",easyFlag=FALSE,verbose=TRUE)
>
> and I get the following error message:
>
> Current maximum number of independent variables is 50000
>  You need to increase the global variable MAX_NVAR_OFFSET to 58531
>  This can be done by putting the line
>    'gradient_structure::set_MAX_NVAR_OFFSET(58531);'
>  before the declaration of the gradient_structure object.
> Error in glmm.admb(dur ~ 1, random = ~group, group = "id", data = dat,  :
>  The function maximizer failed
>
> I've done some reading, mainly on the admb-project website and posts
> on this mailing list, and tried modifying the 'gradient_structure'
> line in the TOP_OF_MAIN_SECTION in the nbmm.tpl file in my R library,
> as I think is suggested... but I get the same error message as if
> nothing had been changed. I would greatly appreciate it if someone
> could clarify if I'm doing something wrong, or if it actually isn't
> possible to change the gradient_structure when running glmmADMB
> through R. By the way, I have no problems running the same model with
> "random=~1".
>
> Thank you in advance for any help.
> All the best,
>
> Raff
>
> --
> Rafael Mares
> Large Animal Research Group (LARG)
> Department of Zoology
> University of Cambridge
> Downing Street
> Cambridge
> CB2 3EJ
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