Prev 14807 / 20628 Next

Unable to standardize glmmADMB global model

Ben Bolker

Tue, Aug 16, 2016 4:55 AM

You can *scale* the offsets if you like, i.e. change them by a
multiplicative factor (thus changing the effective area unit for which
you were modeling counts), but *centering* them doesn't make sense --
as you've noticed.

On Tue, Aug 16, 2016 at 7:40 AM, Aoibheann Gaughran <gaughra at tcd.ie> wrote:

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

Thread (10 messages)

Aoibheann Gaughran Unable to standardize glmmADMB global model Aug 15 Ben Bolker Unable to standardize glmmADMB global model Aug 15 Aoibheann Gaughran Unable to standardize glmmADMB global model Aug 15 Ben Bolker Unable to standardize glmmADMB global model Aug 15 Aoibheann Gaughran Unable to standardize glmmADMB global model Aug 16 Ben Bolker Unable to standardize glmmADMB global model Aug 16 Aoibheann Gaughran Unable to standardize glmmADMB global model Aug 18 Ben Bolker Unable to standardize glmmADMB global model Aug 18 Aoibheann Gaughran Unable to standardize glmmADMB global model Aug 18 Ben Bolker Unable to standardize glmmADMB global model Aug 18