[R-sig-ME] [R] lme nesting/interaction advice

Kingsford Jones kingsfordjones at gmail.com
Wed May 14 19:31:18 CEST 2008

On Wed, May 14, 2008 at 1:19 AM, Nathaniel Smith <njs at pobox.com> wrote:
> On Wed, May 14, 2008 at 09:28:18AM +0200, Reinhold Kliegl wrote:
>> >  The pdfs that come with the package are, alas, basically useless
>> >  (unless you want to fix bugs in lme4).  The best user docs I'm aware
>> >  of are the short article in the May 2005 R newsletter, and the
>> >  papers/book draft written by Harold Baayen et al and available from
>> >  his webpage.
>> I do not think it is very nice to characterize work as ", alas,
>> basically useless (unless you want to fix bugs in lme4)."  There are
>> many other good uses to them, at least I have not fixed a single bug.
>> Why the pejorative language--especially on this list?
> I should perhaps clarify that I was thinking mainly of the lme4
> vignettes, which are explicitly targeted at implementors.  (If you
> have used them for other purposes, then I'd honestly love to know
> what.)  I see on CRAN that the help pages are also available as a PDF,
> and the help pages are definitely valuable to end-users as a
> reference, but... they don't even document how to write an lmer
> formula.  Obviously this will be fixed sooner or later when someone
> has the time, and fortunately we have the other documents mentioned
> above (also mostly authored or co-authored by Doug) to cover the gap
> until then -- but for now they're not trivial to find.
> My intention wasn't to be pejorative, but simply to provide clear and
> honest information about which documentation was currently useful for
> which purposes.  But I do apologize if my flippant way of doing that
> offended anyone.

I have to disagree with your assessment of the vignettes.  The
documents do contain a lot of theory, but chapters 1-4 of
Implementation.pdf do an excellent job of describing varying types of
data to be fit using mixed models, how to fit the models using lmer,
and the structure of the fitted objects returned.  I see those
examples as far from 'useless'.  What exactly are you looking for?
One way you might find what you're looking for is to google:

"lmer" mixed filetype:pdf


lmer mixed filetype:pdf

The later (without the quotes) will lead to many documents on lme as
well as lmer

Also, although written prior to lmer, Pinheiro and Bates 2000 is still
an excellent resource.  Although I have limited experience with lmer,
for many models it seems the only difference for a useR to specify a
model in lme vs lmer is that the random argument from lme is removed
and the value for the argument is put in parentheses and moved into
the model formula.  For example:

lme(score ~ Machine, data = Machines, random= ~ 0 + Machine|Woker)


lmer(score ~ Machine + (0 + Machine|Worker), data = Machines)

This not the case when fitting models with crossed random effects,
where in lme the random arugment took a somewhat convoluted list, but
in lmer the formulas are straightforward.

Finally, I'd like to point out that sending an email to this list is
essentially the same as sending one directly to Doug Bates, who I
think deserves our gratitude for his tremendous contributions to the R
community, and to the advancement of mixed modeling.


Kingsford Jones

> -- Nathaniel
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