[R-sig-ME] lme4 is now on R-forge

Douglas Bates bates at stat.wisc.edu
Fri Nov 9 22:02:52 CET 2007

Users of the current version of the lme4 package have reported several
problems and, for some time, I have been unresponsive about such reports
or I have made reference to the development version of the package.  Let
me emphasize that I am grateful for the reports and, indeed, have fixed
several of these problems in the development version of the package.
However, I have held off releasing the development version because of
one small problem - it doesn't fit generalized linear mixed models correctly.

I have had to go back and reformulate the model from scratch so that I
can understand it and design the code.  As anyone who has developed
and maintained a large project can attest, the only way to build
trustworthy code (and to maintain your sanity) is to modularize the
code.  It goes without saying that before you can decide how to
modularize the code you must be able to decompose the steps in the
computation.  The development version is designed to handle linear
mixed models, generalized linear mixed models, nonlinear mixed models
and generalized nonlinear mixed models with nested or crossed or
partially crossed random factors.  It has taken me a long time to
decide how all those pieces fit together.  Only in the last couple of
weeks have I have managed to convince myself that I know how it all
fits together.  The task of convincing others remains, and is
decidedly non-trivial, but I feel that I can decompose the
computational steps now.

It will take a while to move from the equations in my lab notebook to
released code and, during that process, I will probably need to
reformulate the slots in the S4 classes.  My method of getting to the
final design of the data structures and algorithms is to keep doing it
wrong 'til I do it right.

So that others have easy access to the development version of the
package I have moved the repository for the development version of
the package to http://R-forge.R-project.org/packages/lme4

Martin and I had planned to do this move in a way that would preserve
the history of the changes from the current repository
but that is not easy to do because of the way that the Matrix and lme4
packages were merged then un-merged.  Thus I have made a clean break
and installed the development version (the one known as gappy-lmer) on
R-forge.  You can access it at the URL given above or as
http://lme4.r-forge.r-project.org/, at the expense of one additional click.

Starting tomorrow you should also be able to install the development
version of the package with

install.packages("lme4", repos = "http://r-forge.r-project.org")

Please be aware that the class representations can change so when
using the development version you should not count on being able to re-use
a fitted model after installing a new version.  You should retain the original
data so you can refit the model if necessary.

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