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]]
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]]
> >
> > ______________________________________________
> > 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
>
>
>
---
This email has been checked for viruses by Avast antivirus software.
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]] > > > > > > ______________________________________________ > > > 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 > > > > > > > > > > --- > 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.