[R] "effects" package issue for lme4's lmer()
kriszmosdossy at gmail.com
Thu Jan 29 21:52:16 CET 2015
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
> 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?
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
> In the development version of the effects package on R-Forge, the default
> 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.
> > -----Original Message-----
> > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of
> > 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
> > version 3.1.2 (2014-10-31) -- "Pumpkin Helmet", lme4 package version
> > effects package version 3.0-3 and lmerTest package version 2.0-20. I am
> > a MacBook Pro OS 10.9.5.
> > I constructed my model using the lmer() function in the lme4 package as
> > 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
> > 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
> > 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
> > raises its unforgiving rainbow head (the "wheel of death" returns and I
> > to Force Quit R).
> > Since updating, I have used the "effects" package with a glmer model I
> > 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
> > 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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