[R-sig-ME] lme vs. lmer

Ben Bolker bolker at ufl.edu
Tue Sep 29 20:02:33 CEST 2009

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 superseded lme or if lme still holds its own?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.

    Ben Bolker

Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bolker at ufl.edu / www.zoology.ufl.edu/bolker
GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc

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