[R-sig-ME] New version of lme4 - memory error

[Andrew Robinson]

Hi Doug,

sorry, it's me having problems again :(

I can install and load the new lme4 package with no trouble, but when
I try to run the examples, I get:



>  require(lme4)
Loading required package: lme4
Loading required package: Matrix
Loading required package: lattice
[1] TRUE
> sessionInfo()
R version 2.4.1 Patched (2007-01-25 r40572) 
i386-unknown-freebsd6.1 

locale:
C

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

other attached packages:
       lme4      Matrix     lattice 
"0.9975-11"  "0.9975-8"   "0.14-16" 
> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
> fm1 <- lmer2(Reaction ~ Days + (Days|Subject), sleepstudy)
Error in as.double(start) : Calloc could not allocate (169499040 of 4)
       memory






Does anyone else find this?  Please let me know what else I can do to
help.

Cheers,

Andrew



On Thu, Jan 25, 2007 at 05:12:00PM -0600, Douglas Bates wrote:
> Version 0.9975-11 of the lme4 package has been uploaded to CRAN.  The
> source package should be available on the mirrors in a day or two and
> binary packages should follow soon after.
> 
> There are several changes in this release of the package.  The most
> important is the availability of a development version of lmer called,
> for the time being, lmer2.  At present lmer2 only fits linear mixed
> models.  Generalized linear mixed models will be added "soon".
> Furthermore there is no mcmcsamp method for a model fit by lmer2.
> This deficiency will also be rectified "soon".  Once I have all the
> capabilities and methods currently available for lmer also available
> for the new representation I will remove the old representation and
> rename lmer2 as lmer.
> 
> The current version of lmer will continue to be available throughout
> the migration process.  You don't have to change anything about your
> use of that function unless you want to try the new one.  It would be
> a good idea, however, to save the data and the call to lmer in
> addition to saving an lmer object, if you so choose, so that you can
> recreate the fitted model when the development version becomes the
> release version.
> 
> The package contains a vignette giving the details of the new implementation.
> 
> The reason I am releasing a development version in parallel with the
> production version is because I would like feedback from useR's
> regarding the development version.  In my experience, testing it
> myself and with colleagues whom I visited recently, I have found that
> lmer2 is faster and more reliable than the current lmer.  In
> particular, on some difficult model fits I have been able to get
> substantially better parameter estimates (i.e. the deviance at the
> lmer2 estimates is perhaps 4 or 5 lower than that at the lmer
> estimates) with lmer2 than I could with lmer.
> 
> If you have fit a linear mixed model using lmer and are willing to try
> it with lmer2 I would appreciate your telling me if the parameter
> estimates are comparable and which fit was faster (use system.time()
> to check).  I'm primarily interested in models fit to large data sets
> or "difficult" fits.
> 
> We have established a new mailing list, R-SIG-mixed-models, for
> discussion of R software to fit mixed-effects models, especially lmer.
>  See https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models for
> information or to subscribe.
> 
> I know that I have said this before but this is the last time that I
> am going to change the underlying representation.  Really - trust me -
> this is the last time.  My theory of software development is expressed
> in a line from an old blues song, "you just keep doing it wrong till
> you do it right".  I'm convinced that this time I have it right.  That
> statement sounds like "famous last words", doesn't it?  :-)
> 
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-- 
Andrew Robinson  
Department of Mathematics and Statistics            Tel: +61-3-8344-9763
University of Melbourne, VIC 3010 Australia         Fax: +61-3-8344-4599
http://www.ms.unimelb.edu.au/~andrewpr
http://blogs.mbs.edu/fishing-in-the-bay/