[R-sig-ME] Unable to standardize glmmADMB global model
Aoibheann Gaughran
gaughra at tcd.ie
Thu Aug 18 15:11:43 CEST 2016
> names(std_data) [1] "field_count" "month_fix" "num_fields" "field_id" "animal" "soc_grp" "habitat"
[8] "habitat2" "monyear" "mon" "season_wt"
"season" "month" "year"
[15] "sex" "age" "ageclass" "soil"
"slope" "elevation" "aspect"
[22] "NSEW" "origarea" "newarea" "HRNewArea"
"HabNewArea" "PropAvlHab" "origperim"
[29] "newperim" "propHRfield" "percentHRfield"
"PropHabfield" "percentHabfield" "field_use" "slopescale"
[36] "aspectscale" "z.month_fix" "z.num_fields" "z.slope"
"z.origarea" "z.PropAvlHab"
On 18 August 2016 at 14:07, Ben Bolker <bbolker at gmail.com> wrote:
>
> what's the results of names(std_data) ?
>
> On 16-08-18 09:05 AM, Aoibheann Gaughran wrote:
> > Hi Ben,
> >
> > I've manually scaled and centered the continuous variables, and just
> > scaled the offset terms. However, I now get the following error message
> > when I attempt to run the model, which appears to related to a
> > subsetting issue?
> >
> > Error in `[.data.frame`(cor_dat, start_pos + (1:x$npar), start_pos + 4
> + :
> > undefined columns selected
> >
> > The revised global model is specified as follows:
> >
> > stdmod12d <- glmmadmb(field_count ~ habitat #categorical
> > + season_wt #cat
> > + sex #cat
> > + ageclass #cat
> > + z.slope #continuous, scaled and centred
> > + NSEW #cat
> > + z.month_fix #continuous, scaled and centred
> > + z.num_fields #continuous, scaled and centred
> > + habitat:ageclass
> > + habitat:sex
> > + offset(log(z.origarea)) #scaled
> > + offset(log(z.PropAvlHab)) #scaled
> > +(1|animal) #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 = std_data)
> >
> > On 16 August 2016 at 12:55, Ben Bolker <bbolker at gmail.com
> > <mailto:bbolker at gmail.com>> wrote:
> >
> > 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
> > <mailto: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
> > <mailto: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 <mailto: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
> > <mailto: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 <mailto: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
> > <mailto:R-sig-mixed-models at r-project.org> mailing list
> > >> >> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> > <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 <tel:%2B353%20%2886%29%203812615>
> > >
> > >
> > >
> > >
> > > --
> > > Aoibheann Gaughran
> > >
> > > Behavioural and Evolutionary Ecology Research Group
> > > Zoology Building
> > > School of Natural Sciences
> > > Trinity College Dublin
> > > Dublin 2
> > > Ireland
> > > Phone: +353 (86) 3812615 <tel:%2B353%20%2886%29%203812615>
> >
> >
> >
> >
> > --
> > 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
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