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

[Aoibheann Gaughran]

Hi Ben,

Im proceeding by standardizing by hand.  However, I need to include offsets
in my model for origarea and PropAvlHab i.e. offset(log(z.origarea)) but
logging the standardized varible produced NaNs due to the presence of
negative numbers, ditto with z.PropAvlHab. Is there a way around this? Do I
need to also standardize the offset terms or can I leave them in their
unstandardized form?

Many thanks,

Aoibheann

On 15 August 2016 at 15:47, Ben Bolker <bbolker at gmail.com> wrote:

> Hmm.  Surprising/hard to diagnose.
>
> 'standardize' doesn't do anything very fancy - it standardizes the
> input variables as described by ?arm::standardize and *refits* the
> model (I've always been a little disappointed that it doesn't
> standardize by figuring out how to transform the *parameters*, which
> is straightforward in principle although it can be tricky to figure
> out how to deal with input variables that lead to multiple predictor
> variables, e.g. polynomials).  I'd be curious to know what's going on,
> but in your place I would
>
> (1) try standardizing by hand, e.g.
>
> std_data <- transform(data,
>       z.season.wt = scale(season.wt),
>      ...)
>
> and refit yourself.
>
> (2) see if it happens to work with glmmTMB (a simple example does).
>
>   Ben Bolker
>
>
>
>
> On Mon, Aug 15, 2016 at 10:37 AM, Aoibheann Gaughran <gaughra at tcd.ie>
> wrote:
> > 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) = 24
> > In addition: Warning messages:
> > 1: In log(z.PropAvlHab) : NaNs produced
> > 2: 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
>



-- 
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]]