On Fri, Nov 11, 2011 at 10:22 AM, Michael Lawrence <
lawrence.michael@gene.com> wrote:

> I have spoken with him about this, and I wasn't sure if it was worth it.
> Much of the documentation we write is pretty free-form. I am not sure how
> that could be inlined. Maybe it's just the wrong style? Do people really
> like putting all that documentation into their source code? Literate
> programming is nice for a data analysis in a vignette, but I'm not so sure
> about IRanges. Folding might help. What's so bad about Rd anyway? I guess
> I'm just more of a "use the source, Luke" kind of guy and like direct
> control over the output.
>
> What would be really nice is a way to generate documentation on methods and
> classes dynamically, as they are registered. Some sort of alternative to
> always calling showMethods, getClass, etc.
>
>
I second this.  And I conjecture that tools to create useful documentation
of this sort are found
in part in the installation and checking software.  Robert's book has code
for class graph generation IIRC and
that is relevant.  Class residency in packages is relevant along with
package dependence graphs.

I find that rapidly generated/surveyed overviews of software structure and
component relationships can be valuable in planning development or workflow
structure, can be hard to get, but should be relatively easily created via
calls into the system.  That's where I would put general documentation
effort -- if I had the time.


> Michael
>
> On Fri, Nov 11, 2011 at 6:42 AM, Steve Lianoglou <
> mailinglist.honeypot@gmail.com> wrote:
>
> > Hi devs,
> >
> > Hadley is in the midst of trying to get roxygen2 to better handle S4
> > class/methods.
> >
> > I thought there would be some folks here (hi bioc-core) who would be
> > well suited to give useful feedback given the monumental documentation
> > in some of the bioconductor packages.
> >
> > If anyone has time to share some feedback, I'm sure it'd make his end
> > result much better and would be a large boon to the R community at
> > large, since I think roxygen goes a long way to making writing
> > documentation a lot less painful :-)
> >
> > Here is his post:
> >
> >
> http://lists.r-forge.r-project.org/pipermail/roxygen-devel/2011-November/000318.html
> >
> > Cheers,
> > -steve
> >
> > --
> > Steve Lianoglou
> > Graduate Student: Computational Systems Biology
> >  | Memorial Sloan-Kettering Cancer Center
> >  | Weill Medical College of Cornell University
> > Contact Info: http://cbio.mskcc.org/~lianos/contact
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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