[R] "effects" package issue for lme4's lmer()
John Fox
jfox at mcmaster.ca
Thu Jan 29 23:09:14 CET 2015
Dear Krisztina,
I'm glad this worked out. I've cc'ed my response to r-help and Sandy Weisberg so everyone following this thread can see the outcome.
Best,
John
> -----Original Message-----
> From: Krisztina Mosdossy [mailto:kriszmosdossy at gmail.com]
> Sent: January-29-15 4:51 PM
> To: jfox at mcmaster.ca
> Subject: Re: [R] "effects" package issue for lme4's lmer()
>
> Hi John,
>
> Eureka! Apparently I'm set up to build R packages and the code worked.
>
> Thank you very much!
>
> -Krisz
>
> On Thu, Jan 29, 2015 at 4:29 PM, John Fox <jfox at mcmaster.ca> wrote:
>
>
> Dear Krisztina,
>
> I don't think that you mentioned that you were using Mac OS X and if
> you did I missed it. Presumably allEffects() still doesn't work because you
> didn't install the development version of effects.
>
> R-Forge doesn't build binary packages for Mac OS X. If you're set up
> to build R packages on your Mac you should be able to use
>
> install.packages("effects", repos="http://R-Forge.R-project.org",
> type="source")
>
> If not, then you'll have to wait until the new version is moved to
> CRAN. An alternative would be to bypass allEffects() and plot each effect of
> interest individually using Effect() with KR=FALSE.
>
> I hope this helps,
> John
>
>
> > -----Original Message-----
> > From: Krisztina Mosdossy [mailto:kriszmosdossy at gmail.com]
> > Sent: January-29-15 3:52 PM
> > To: jfox at mcmaster.ca
> > Cc: r-help at r-project.org; Sandy Weisberg
> > Subject: Re: [R] "effects" package issue for lme4's lmer()
> >
> > Hello John,
> >
> > Thank you for your prompt reply!
> >
> > Unfortunately, I get the following message when trying to
> download the
> > "effects" package from R-forge (and allEffects() doesn't work):
> >
> >
> > Warning: unable to access index for repository http://R-Forge.R-
> > project.org/bin/macosx/mavericks/contrib/3.1
> > package ‘effects’ is available as a source package but not as a
> binary
> > Warning message:
> > package ‘effects’ is not available (for R version 3.1.2)
> >
> >
> >
> > I don't think I have ever downloaded a packed from R-Forge
> before, so I am
> > unsure of how to resolve this. Words of wisdom?
> >
> > Thank you!
> >
> > -Krisz
> >
> > On Thu, Jan 29, 2015 at 2:36 PM, John Fox <jfox at mcmaster.ca>
> wrote:
> >
> >
> > Dear Krisztina,
> >
> > Thank you for your kind remarks about the effects package.
> >
> > The issue is almost surely the slow computation of Kenward-
> Roger
> > standard
> > errors for the effects, which we compute by default (KR=TRUE)
> for a
> > linear
> > mixed model fit by lmer(). This problem is compounded by a bug
> in
> > allEffects(), but not effect() or Effect(), that prevents changing
> KR to
> > FALSE.
> >
> > In the development version of the effects package on R-Forge,
> the
> > default is
> > changed to KR=FALSE and the bug in allEffects() is fixed. Until
> the
> > effects
> > package is updated on CRAN, you should be able to install the
> > development
> > version from R-Forge via
> >
> > install.packages("effects", repos="http://R-Forge.R-
> project.org")
> >
> > I apologize for this problem.
> >
> > Best,
> > John
> >
> >
> > > -----Original Message-----
> > > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf
> Of
> > Krisztina
> > > Mosdossy
> > > Sent: January-29-15 10:44 AM
> > > To: r-help at r-project.org
> > > Subject: [R] "effects" package issue for lme4's lmer()
> > >
> > > Hello fine R folks,
> > >
> > > I am a big fan of the "effects" package as it enables me to
> visualize
> > my
> > > GLMM's quite nicely and with ease. I am, however, unable to
> find a
> > way to
> > > use the effect() or allEffects() functions with my recent lmer
> > model.
> > >
> > > I just updated R, lmerTest and effects packages the other day.
> I am
> > using
> > R
> > > version 3.1.2 (2014-10-31) -- "Pumpkin Helmet", lme4 package
> > version
> > 1.1-7,
> > > effects package version 3.0-3 and lmerTest package version
> 2.0-20.
> > I am
> > using
> > > a MacBook Pro OS 10.9.5.
> > >
> > > I constructed my model using the lmer() function in the lme4
> > package as
> > well
> > > as the lmerTest() function:
> > >
> > > m.proc3.2<-
> > >
> >
> lmerTest::lmer(Duration~InvertAvg2012+NInvertSample2012+RipeFruit2012
> > > +AvgFrass2012+FocalDuration+(1|Group/Animal)+(1|Type),
> > > data=datsc)
> > >
> > >
> > > Where "Duration" is a continuous response variable, while
> each
> > fixed
> > > explanatory variable is continuous and each random variable is
> > categorical.
> > > I scaled each continuous explanatory variable.
> > >
> > > The problem I am having:
> > >
> > >
> > > effect(m.proc3.2)
> > >
> > > or
> > >
> > > allEffects(m.proc3.2)
> > >
> > >
> > > provides the lovely "wheel of death", my computer starts
> heating
> > up and R
> > is
> > > no longer responsive (for this reason I end up having to Force
> Quit
> > R).
> > > I also tried the above code without lmerTest() just in case, but
> the
> > beach
> > ball
> > > raises its unforgiving rainbow head (the "wheel of death"
> returns
> > and I
> > have
> > > to Force Quit R).
> > >
> > > Since updating, I have used the "effects" package with a glmer
> > model I
> > have
> > > and allEffects() works wonders. It's only with the lmer() that
> I'm
> > having
> > > issues. I have searched and searched cyberspace and no one
> else
> > seems to
> > > be having this problem. In fact, the "effects" package is often
> > recommended
> > > when seeking visual representation of one's lmer model. Am I
> > missing
> > > something?
> > >
> > >
> > > Thank you for your time!
> > >
> > >
> > > Krisztina Mosdossy, M.A.
> > >
> > > Department of Anthropology
> > >
> > > University of Calgary
> > >
> >
> > > [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
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> >
> >
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