[R] How to solve allocation problem in lme() analysis?

Spencer Graves spencer.graves at pdf.com
Fri Dec 2 03:02:45 CET 2005

	  1.  Since your example is incomplete, I can't easily replicate the 
phenomenon.  This limits me to general comments and brainstorming on 
things I might try.

	  2.  Have you tried "lmer" in library(lme4)?  The syntax will be 
different, but it's a different algorithm and can handle problems that 
crash "lme".  This may or may not apply to you.  For documentation on 
this, see Douglas Bates (2005) "Fitting linear mixed models in R. R 
News, 5(1):27-30, available from www.r-project.org -> newsletter.  See 
also "Implementation.pdf" in the "doc" subdirectory under "lme4" in the 
"library" folder of your R installation;  if you are not using Windows, 
I don't know if this is how you find this document.

	  3.  What is "L" in your model?  If it is a factor with many levels, 
this might explain the warning you got:  "Fewer observations than random 
effects ... ."

	  4.  Can you simplify the problem and still get the same error?  For 
example, do you get the same problem after deleting "F1+F2" from 
"fixed"?  If you can produce a simple example with a few lines of R code 
that generates a pseudo-random data set and send that to this list (as 
suggested in the posting guide! "www.R-project.org/posting-guide.html"), 
you might get a more useful reply.  Or you might just solve your problem 
in the course of trying to construct such an example.

	  5.  Have you consulted Pinheiro and Bates (2000) Mixed-Effects Models 
in S and S-Plus (Springer)?  I couldn't get started with "lme" until I 
got that book and started reading it.

	  hope this helps.
	  spencer graves

Petar Milin wrote:

> Hello!
> I am running analysis on the data from 4 experiments, with approximately
> 4600 rows (cases). My working model is:
> fitA1 = lme(RT~F1+F2+L,random=~1|Experiment/Subject,data=data)
> Model works very fine, but if I try to check whether the effect of L
> depends on Experiments/Subjects with:
> fitA2 = lme(RT~F1+F2+L,random=~1+L|Experiment/Subject,data=data)
> [with the idea to make: anova(fitA1,fitA2)]
>>analysis crashes with the message:
>>Error: cannot allocate vector of size 2481574 Kb
>>In addition: Warning message:
>>Fewer observations than random effects in all level 2 groups in:
>>lme.formula(RT ~ F1 + F2 + L, random = ~1 + L | Experiment/Subject,
> Can anyone help me with this issue? Thanks in advance.
> Sincerely,
> Petar Milin
> Assistant Professor
> Department of Psychology
> University of Novi Sad
> Serbia and Montenegro
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Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
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