lmer formula syntax?

On Wed, Feb 2, 2011 at 3:43 PM, Colin Wahl <biowahl at gmail.com> wrote:

I too have found the Bate's book draft helpful, but I have not been able to
get the lme4a package installed. The best description I have found to do so
is:
http://kmyu.wordpress.com/2010/12/04/installing-lme4a-in-r-mac-osx-10-6-4/

I'm understanding that the lme4a package is dependent on a number of
packages: RcppArmadillo, minqa and MatrixModels (available on CRAN
respositories) and Rcpp version 0.8.8.1 or later (which is not; version
0.8.6 is).

(Actually it doesn't depend on RcppArmadillo).

You must be using Mac OS X.  If you check at
cran.r-project.org/web/packages/Rcpp you will see that the Windows
binary and the source code packages are at version 0.9.0 but the Mac
OS X version is only at 0.8.6, which is rather old.  I'm not sure what
the problem is as Romain develops on a Mac OS X system and he can't
reproduce the error.

However, you don't really need lme4a for most of the examples in the
book.  The lme4 package can't handle the profile-related material, but
the rest of the examples should be okay.  The output looks slightly
different but the parameter estimates should be essentially the same.

Apparently it is available on something called an SVN
respository. Im getting into language I am unfamiliar with. If you can
provide some advice to aid my ignorance in installing this package I could
likely get a lot more out of the book draft.

Thank for you time and assistance.

On Tue, Feb 1, 2011 at 6:34 PM, George Wang <pseudotelphusa at gmail.com>wrote:

I am also quite new to lme4 myself, so I'll just add one thing to Toby's
earlier answer.

On Tue, Feb 1, 2011 at 5:14 PM, Colin Wahl <biowahl at gmail.com> wrote:

Dear r-sig-mixed-models List,

[snip]

Secondarily: I have read a few times that "wshed/stream" is
interchangeable
with  "wshed:stream" which is a meaningless interaction. Also I've seen
that
random effects are specified as (a|b) where a is a covariate and b is a
grouping factor. Does having 1 as a covariate simply specifying an
intercept
of 1? What is the purpose of placing a factor in the place of 1 as a
covariate? OR is there a nice complete summary tutorial that I've missed.

A specification of (1|b) means that the model is fit with a random effect
for each level of b (simple scalar random effect). The "a" in (a|b) is a
correlated random effect along with "b", with both an intercept and slope.
You can also make them uncorrelated, with slope only for a.

The draft of Prof. Doug Bate's book covers many useful basics on lmer, and
is where I learned most of mine.
http://lme4.r-forge.r-project.org/book/

HTH
George

I'm looking forward to hearing any comments.

Thank you,
--
Colin Wahl
Department of Biology
Western Washington University
Bellingham, WA 98225
ph: 360-391-9881

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