lme vs. lmer
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 I am curious if lmer from lme4 has superseded lme or if lme still holds its own?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
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