[R-sig-ME] Version of lme4 on R-forge

Douglas Bates bates at stat.wisc.edu
Thu Apr 24 15:17:55 CEST 2008

There has been some discussion on this list about what is the "most
recent" version of the lme4 package.  The version on CRAN is
comparatively old.  Several months ago I made some radical changes in
the internal representation of the model and I am still working on
providing all the earlier capabilities under this new representation.
This is the version on R-forge.  It is much more advanced than the
version on CRAN in the design and even in the theory but there are
still areas where its functionality is incomplete.  In particular, the
mcmcsamp function in the R-forge version doesn't work well for models
where some of the variance components are near zero.  I think I have a
way out of that but it will involve more development and coding and

If I release the R-forge version to CRAN some of the code that is
documented in books like Harald Baayen's "Analyzing Linguistic Data"
and Gelman and Hill's "Data Analysis Using Regression and
Multilevel/Hierarchical Models" will cease to function or, worse,
produce incorrect results.

In general I think that users are better off with the version on
R-forge except for the long-standing problem of how to come up with
p-values on fixed-effects terms.  This is why I get frustrated with
this issue of p-values and degrees of freedom.  There are many good
things that could be done with the version of lme4 on R-forge.  In
particular, the ability to fit models to large data sets with crossed
or partially crossed factors for random effects is revolutionary.
Other software can't do that.  But that doesn't matter.  The only
important issue is being able to produce the "correct" degrees of
freedom on some tinker-toy text book example.

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