ranef() on Mac OS X - R-SIG-mixed-models

Tue, Oct 19, 2010 9:56 AM #

Dear Chris,

I've had problems similar to this before, and it's often due to having nlme loaded along with lme4. I use a Mac. I see from your sessionInfo() that you had nlme loaded on Mac, but not Ubuntu. I'd trying detaching:

Error in UseMethod("ranef") : 
  no applicable method for 'ranef' applied to an object of class "mer"

$Subject
    (Intercept)        Days
308   2.2571870   9.1992523
309 -40.3984020  -8.6211497

etc.

Hope that works.

- Malcolm


Dr Malcolm Fairbrother
Lecturer
School of Geographical Sciences
University of Bristol

Message: 4
Date: Tue, 19 Oct 2010 11:31:18 -0500
From: Christopher Desjardins <desja004 at umn.edu>
To: r-sig-mixed-models at r-project.org
Subject: [R-sig-ME] ranef() on Mac OS X
Message-ID:
	<AANLkTin=ksZK=5eC30fHiaY9OH-Y3ExaU=5yktc0DB9O at mail.gmail.com>
Content-Type: text/plain

I am unable to use the ranef() function on a lmer function on a Mac. I get
the following error:

fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
ranef(fm1)

Error in UseMethod("ranef") :
 no applicable method for 'ranef' applied to an object of class "mer"

sessionInfo()

R version 2.11.1 (2010-05-31)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] plyr_1.2.1         nlme_3.1-96        lme4_0.999375-34
Matrix_0.999375-39 lattice_0.18-8     foreign_0.8-40

loaded via a namespace (and not attached):
[1] grid_2.11.1   stats4_2.11.1 tools_2.11.1

This works as expected on Ubuntu 10.10 64 bit (see below). I built the lme4
package from source on the Mac and I know that lme4 has had some issues on
Mac for a while (i.e. it hasn't been available as a binary for some time). I
just wanted to post this here to see if this was either a new bug, something
already documented, or something that I've overlooked. Googling 'ranef lme4
Mac' brought me to this thread
https://stat.ethz.ch/pipermail/r-sig-mixed-models/2010q3/004091.html ... but
the author was able to use the ranef() function.

Thanks,
Chris


#################
### From Linux ###
#################

fm1 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy)
ranef(fm1)

$Subject
   (Intercept)
308   40.787403
309  -77.856603
310  -63.114282
330    4.406841
331   10.217114
332    8.221982
333   16.501988
334   -2.997253
335  -45.286227
337   72.189222
349  -21.198168
350   14.112641
351   -7.862933
352   36.381719
369    7.037018
370   -6.363279
371   -3.294571
372   18.117387

sessionInfo()

R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu

locale:
[1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
[3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
[5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8       LC_NAME=C
[9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] lme4_0.999375-35   Matrix_0.999375-40 lattice_0.18-8

loaded via a namespace (and not attached):
[1] grid_2.11.1   nlme_3.1-96   stats4_2.11.1 tcltk_2.11.1  tools_2.11.1




-- 
Christopher David Desjardins
Ph.D. student, Quantitative Methods in Education
M.S. student, Statistics
University of Minnesota

	[[alternative HTML version deleted]]



------------------------------

Message: 5
Date: Tue, 19 Oct 2010 11:44:58 -0500
From: Douglas Bates <bates at stat.wisc.edu>
To: Christopher Desjardins <desja004 at umn.edu>
Cc: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] ranef() on Mac OS X
Message-ID:
	<AANLkTimOmPM0cdw6zLFjrSRrF_M_GgT9d3Q4RYM0F8WA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Notice that you have different versions of the lme4 package on Ubuntu
and on the Mac.  For some reason the lme4 package is failing a test on
Mac OS X only and we haven't been able to diagnose why the -35 version
fails there.  Also, we haven't been able to reproduce this on other
operating systems and we can't decide why it should fail on Mac OS X
unless it is an obscure memory issue.  As neither Martin nor I use Mac
OS X we aren't able to debug the issue.  Other folks have looked at it
but all they can say is that it is failing, no idea why.  We even
tried to bypass the test on the Mac but that doesn't seem to have
worked either.

I'm open to suggestions from the list on what can be done about lme4
and Mac OS X.  If you look at the test results for the package on
CRAN, e.g.

http://cran.us.r-project.org/web/checks/check_results_lme4.html

you will see that Mac OS X is the only system on which there is a
problem and the test on which it fails doesn't make sense for it to
fail.  The only difference between the two models being compared is
that they were generated from slightly different formulas but the
models are identical once the formula is parsed.

On Tue, Oct 19, 2010 at 11:31 AM, Christopher Desjardins
<desja004 at umn.edu> wrote:

I am unable to use the ranef() function on a lmer function on a Mac. I get
the following error:

fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
ranef(fm1)

Error in UseMethod("ranef") :
?no applicable method for 'ranef' applied to an object of class "mer"

sessionInfo()

R version 2.11.1 (2010-05-31)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base

other attached packages:
[1] plyr_1.2.1 ? ? ? ? nlme_3.1-96 ? ? ? ?lme4_0.999375-34
Matrix_0.999375-39 lattice_0.18-8 ? ? foreign_0.8-40

loaded via a namespace (and not attached):
[1] grid_2.11.1 ? stats4_2.11.1 tools_2.11.1

This works as expected on Ubuntu 10.10 64 bit (see below). I built the lme4
package from source on the Mac and I know that lme4 has had some issues on
Mac for a while (i.e. it hasn't been available as a binary for some time). I
just wanted to post this here to see if this was either a new bug, something
already documented, or something that I've overlooked. Googling 'ranef lme4
Mac' brought me to this thread
https://stat.ethz.ch/pipermail/r-sig-mixed-models/2010q3/004091.html ... but
the author was able to use the ranef() function.

Thanks,
Chris


#################
### From Linux ###
#################

fm1 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy)
ranef(fm1)

$Subject
? ?(Intercept)
308 ? 40.787403
309 ?-77.856603
310 ?-63.114282
330 ? ?4.406841
331 ? 10.217114
332 ? ?8.221982
333 ? 16.501988
334 ? -2.997253
335 ?-45.286227
337 ? 72.189222
349 ?-21.198168
350 ? 14.112641
351 ? -7.862933
352 ? 36.381719
369 ? ?7.037018
370 ? -6.363279
371 ? -3.294571
372 ? 18.117387

sessionInfo()

R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu

locale:
?[1] LC_CTYPE=en_US.utf8 ? ? ? LC_NUMERIC=C
?[3] LC_TIME=en_US.utf8 ? ? ? ?LC_COLLATE=en_US.utf8
?[5] LC_MONETARY=C ? ? ? ? ? ? LC_MESSAGES=en_US.utf8
?[7] LC_PAPER=en_US.utf8 ? ? ? LC_NAME=C
?[9] LC_ADDRESS=C ? ? ? ? ? ? ?LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base

other attached packages:
[1] lme4_0.999375-35 ? Matrix_0.999375-40 lattice_0.18-8

loaded via a namespace (and not attached):
[1] grid_2.11.1 ? nlme_3.1-96 ? stats4_2.11.1 tcltk_2.11.1 ?tools_2.11.1




--
Christopher David Desjardins
Ph.D. student, Quantitative Methods in Education
M.S. student, Statistics
University of Minnesota