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 <j...@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-boun...@r-project.org] On Behalf Of > Krisztina > > Mosdossy > > Sent: January-29-15 10:44 AM > > To: r-help@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]] > > > > ______________________________________________ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting- > > guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > --- > This email has been checked for viruses by Avast antivirus software. > http://www.avast.com > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
