[Rd] suggesting \alias* for Rd files (in particular for S4 method documentation)

Martin Morgan mtmorgan at fhcrc.org
Thu Aug 30 14:54:16 CEST 2007

Hi Oleg --

On the usefulness of write.image,Image,character-method, in the end I
really want documentation on specific methods. Maybe the issue is one
of presentation?


or, in a little more dynamic world, a '+' in front of write.image to
expand the methods list.

alias* is a little strange, because it implies you're writing
documentation, but then hiding easy access to it! This is not a strong
argument against introducing alias*, since no one is forced to use it.

It also suggests that your documentation is organized by generic,
which might also be a bit unusual -- I typically have an object (e.g.,
an Image) and wonder what can be done to it (e.g., write it to
disk). This suggests associating method documentation with object
documentation. Multiple dispatch might sometimes make this difficult
(though rarely in practice?). Separately documenting the generic is
also important.


Oleg Sklyar <osklyar at ebi.ac.uk> writes:

> Hi,
> I do not know if everybody finds index pages of the html-formatted R
> help useful, but I know I am at least not the only one who uses them
> extensively to get the overview of functions and methods in a package
> (even for my own package). Problems arise, however, if a lot of S4
> methods need to be documented blowing out the index with (generally
> irrelevant) entries like:
> write.image,Image,missing-method
> write.image,Image,character-method
> instead of a simple "write.image". I also do not believe anyone really
> does something like "help(write.image,Image,missing-method)" on the
> command line, thus these structures are more for internal linking than
> for users.
> Therefore, I would suggest to introduce a modification of the \alias
> keyword, that would do all the same as the standard \alias keyword, yet
> it would *hide* that particular entry from the index. Reasonable
> construction could be something like \alias*{} yielding
> \alias{write.image}
> \alias*{write.image,Image,missing-method}
> \alias*{write.image,Image,character-method}
> Alternatively:
> \alias{write.image}
> \alias[hide]{write.image,Image,missing-method}
> \alias[hide]{write.image,Image,character-method}
> Any comments?
> For me, the current way around is to avoid usage sections with \S4method
> all together, substituting them with pairs of
> \section{Usage}{\preformatted{
> }}
> \section{Arguments}{
> }
> and putting all aliases marked above with * into internals, which is
> definitely not the best way of going around documentation and
> code/documentation mismatches.
> Best regards,
> Oleg
> -- 
> Dr. Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-464466
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> R-devel at r-project.org mailing list
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Martin Morgan
Bioconductor / Computational Biology

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