[R-sig-ME] lme vs. lmer

Douglas Bates bates at stat.wisc.edu
Tue Sep 29 20:36:06 CEST 2009

On Tue, Sep 29, 2009 at 1:17 PM, Christopher David Desjardins
<desja004 at umn.edu> wrote:
> Thanks Ben. I knew about the discussion with the dfs and p-values. I guess
> what I was really wondering was if lme was deprecated, which you've
> answered.
> Chris

As Ben said, lmer does not currently allow for parameterized
correlation structures or parameterized weight functions as lme does.
If you need those you should use lme.  For models that can be fit by
both I would use lmer.  It is more reliable and usually faster.

> Ben Bolker wrote:
>> Christopher David Desjardins wrote:
>>> I've started working through Pinheiro & Bates, 2000 and noticed the use
>>> of lme from the nlme package. I am curious if lmer from lme4 has superseded
>>> lme or if lme still holds its own? The reason I ask is that I have taken a
>>> few classes where we've solely used lmer and just read about lme today. If
>>> both functions are on equal footing, can the p-values from lme be trusted?
>>> Thanks!
>>> Chris
>>  You should read the extended discussion of p-values, degrees of
>> freedom, etc. that is on the R wiki (I think) and referenced from the R
>> FAQ.  At least in my opinion, (n)lme is still fine (and indeed necessary
>> at this stage for fitting heteroscedastic and correlated models).  The
>> df/p-value estimates, however, are "use at your own risk" -- you'll have
>> to read the literature and decide for yourself.
>>  I still think there's room for someone to implement (at least)
>> Satterthwaite and (possibly) Kenward-Roger corrections, at least for the
>> sake of comparison, but I'm not volunteering.
>>  cheers
>>    Ben Bolker
> --
> Christopher David Desjardins, Ph.D. Student
> Quantitative Methods in Education
> Department of Educational Psychology
> University of Minnesota
> http://cddesjardins.wordpress.com/
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