[R] small issue with densityplot

Deepayan Sarkar deepayan.sarkar at gmail.com
Wed Aug 22 00:08:17 CEST 2007

On 8/21/07, Douglas Bates <bates at stat.wisc.edu> wrote:
> On 8/21/07, Horace Tso <Horace.Tso at pgn.com> wrote:
> > Deepayan, you're right. Now I realize anyone could write a densityplot function to apply on a different class of objects. I guess I should write to the author of lme4 which from what I could see does not describe a densityplot. By the way, it is used in Baayen, Davidson, and Bates (2006).
> You're right.  It's my bad for not documenting that the coda package
> is required for plots of the results of mcmcsamp.  I was trying to
> piggy-back on the work that the authors of the coda package had done
> on diagnostics, etc.  It was actually Deepayan and I who added the
> lattice-based plots to the coda package for exactly this purpose (did
> you remember that, Deepayan?).

I do remember that, but my point remains:

(1) densityplot is a generic in lattice and documented as such.

(2) mcmcsamp produces an object of class "mcmc" defined in coda, and
this is documented in help(mcmcsamp), which even uses densityplot for
its examples after attaching coda.

(3) densityplot.mcmc is documented in coda.

which all seems to be as it should be (except maybe ?densityplot.mcmc
should additionally have an alias for densityplot). The only confusing
aspect I see is that lme4 does not require or import coda, even though
mcmcsamp produces objects of a class that is supposedly from coda. I
realize that ownership of S3 classes is not well defined, but wouldn't
that be the logical thing to do? The original problem wouldn't have
come up if this were true.


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