[R-sig-ME] lme vs lme4

[Ben Bolker]

Jim Maas <j.maas at ...> writes:

> We are attempting to compare some results using lme and lme4.  I'm 
> relatively new to this so could well be asking questions that are overly 
> simplistic or naive, if so please inform.
> 
> We have an example that works with nlme(lme) and specifying the weights 
> as the function varConstPower, however when we try to do a slightly more 
> specific analysis using lme4(lmer) it doesn't seem to have the 
> varConstPower function built it.  Is in nonsensical to build it into 
> lme4?  It might well have some shortcomings/compromises. Is there a way 
> we could accomplish the same thing with lme4 via some R coding or any 
> other method?

   It's not nonsensical, but it's way down the priority list for
the lme4 developer(s), so I wouldn't hold your breath.

  I guess my question would be: what are the advantages of lme4
for your particular analysis (i.e. reasons to use lme4 instead
of nlme)?  The main ones that I can think of are (1) speed and
(2) handling of crossed random effects.  For #1, you might consider
ASREML-R (I'm not particularly familiar with it, and I mostly
work with GLMMs, for which ASREML has some lacunae, but I've been
impressed by some of the posts at http://www.quantumforest.com/ ...)
For #2, it is *possible* [although clunky/slow] to implement crossed
random effects in (n)lme.

  See http://glmm.wikidot.com/faq#lme-comp (for example)