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]]
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]]
>
> ______________________________________________
> R-help at 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.
---
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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]] > > > > ______________________________________________ > > R-help at 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]]