[R-sig-ME] Unable to standardize glmmADMB global model

[Aoibheann Gaughran]

Thanks Ben, I ran the code and got the following error and warnings:-

Error in glmmadmb(formula = field_count ~ habitat + season_wt + c.sex +  :
  rank of X = 16 < ncol(X) = 24In addition: Warning messages:1: In
log(z.PropAvlHab) : NaNs produced2: In glmmadmb(formula = field_count
~ habitat + season_wt + c.sex +  :
  NAs removed in constructing fixed-effect model frame: you should
probably remove them manually, e.g. with na.omit()


The original PropAvlHab summary is as follows:-

> summary(dframe1$PropAvlHab)     Min.   1st Qu.    Median      Mean   3rd Qu.      Max.
0.0000123 0.1123000 0.4041000 0.4078000 0.6818000 1.0000000

Aoibheann


On 15 August 2016 at 15:12, Ben Bolker <bbolker at gmail.com> wrote:

> 'standardize' is a function from the arm package.
>
> I've just hacked glmmADMB a little bit so this should work:
>
> library(devtools)
> install_github("bbolker/glmmADMB")  ## install latest version
> library(arm)
> arm:::standardize.default(fitted_model$call)
>
>
>
> On Mon, Aug 15, 2016 at 5:06 AM, Aoibheann Gaughran <gaughra at tcd.ie>
> wrote:
> > Hello Mixed-Modellers,
> >
> > I have getting the following error message when trying to standardize my
> > global glmmadmb model for dredging:
> >
> > Error in (function (classes, fdef, mtable)  : unable to find an inherited
> > method for function ‘standardize’ for signature ‘"glmmadmb"’
> >
> > Is it not possible to standardise a glmmadmb model or is the problem with
> > the structure of the model itself?
> >
> > globalmod    <- glmmadmb(field_count ~ habitat
> > #categorical - 7 levels
> >                      + season_wt
> >                                          #categorial - 3 levels
> >                      + sex
> >                                               #categorial - 2 levels
> >                      + ageclass
> >                                            #categorial - 3 levels
> >                      + slope
> >                                              #continuous, not scaled nor
> > centred
> >                      + NSEW
> >                                           #catagorical - 4 levels
> >                      + month_fix
> >                                           #continuous, not scaled nor
> > centred,
> >                      + num_fields
> >                   #continuous, not scaled nor centred
> >                      + habitat:ageclass
> >                      + habitat:sex
> >                      + offset(log(origarea))
> >                      + offset(log(PropAvlHab))
> >                      +(1|individual_id)
> >                                            #repeated obs from same
> > individual
> >                      +(1|field_id)
> >                                               #repeated obs in same
> field,
> >                      family="nbinom",
> >                      zeroInflation=TRUE,
> >                      admb.opts=admbControl(shess=FALSE,noinit=FALSE),
> >                      debug=TRUE,
> >                      data = dframe1)
> >
> > no of observations =9220
> >
> > Many thanks,
> >
> > --
> > Aoibheann Gaughran
> >
> > Behavioural and Evolutionary Ecology Research Group
> > Zoology Building
> > School of Natural Sciences
> > Trinity College Dublin
> > Dublin 2
> > Ireland
> > Phone: +353 (86) 3812615
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-mixed-models at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>



-- 
Aoibheann Gaughran

Behavioural and Evolutionary Ecology Research Group
Zoology Building
School of Natural Sciences
Trinity College Dublin
Dublin 2
Ireland
Phone: +353 (86) 3812615

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