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:kriszmosdo...@gmail.com] > Sent: January-29-15 4:51 PM > To: j...@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 <j...@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:kriszmosdo...@gmail.com] > > Sent: January-29-15 3:52 PM > > To: j...@mcmaster.ca > > Cc: r-help@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 <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 > > > > > > > > > > --- > This email has been checked for viruses by Avast antivirus software. > http://www.avast.com > > > --- This email has been checked for viruses by Avast antivirus software. ______________________________________________ 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.
