From jmc at research.bell-labs.com  Mon May 26 11:45:40 2003
From: jmc at research.bell-labs.com (John Chambers)
Date: Mon May 26 16:46:13 2003
Subject: Documenting classes and methods: was [Rd] Re: R-devel Digest,
	Vol 3, Issue 23
References: <5.2.0.9.1.20030524221045.00abf6c8@imaphost.wehi.edu.au>
Message-ID: <3ED22894.57F62EB7@research.bell-labs.com>

Gordon Smyth wrote:
> 
> I am another person who has had trouble documenting S4 classes and
> (particularly) methods. The methods package itself is pretty cool by the
> way, but it is a pity that there are as yet no guidelines on S4 in the
> "Writing R Extensions" document.
> 
> I have actually put together a guide on S4 documentation myself for the use
> of my own lab which is at http://bioinf.wehi.edu.au/limma/Rdocs.html. I
> don't pretend that the guide is perfect - I can already see problems with
> it - but it has proved adequate so far for our own use (writing the limma
> package) and has gained some more general acceptance from the Bioconductor
> community.
> 
> I found it hard to use the skeleton documentation provided by
> promptMethods. 

The "structure" of the skeletons (the \alias lines especially) are
intended to be used by the help system.  You're not meant to "use" these
directly, much of the time.  It's the case that the tools to work with
the .Rd structure haven't caught up yet, but please don't modify the
skeleton's structure arbitrarily.

> Suppose for example that I wish to document a method for
> generic function 'foo' with argument list (x,y,...) for x of class 'bar1'
> and y of class 'bar2':
> 
> 1. The skeleton .Rd file contains \alias{foo-methods}. If two or more more
> packages document methods for 'foo', they'll all have the same alias entry,
> and the help that a user will get by typing ?"foo-methods" will depend on
> which package happens to have been loaded most recently.

Good point, but related to the behavior of "?".  It's related to a
number of other issues about multiple packages referring to the same
generic function.  Not likely to change for 1.7.1, but likely to be
different in several ways in 1.8

> 
> 2. There seems to be no allowance for documenting extra named arguments for
> this method which are not specified in the generic. There is no usage
> entry, no argument list, and no process for R CMD check to check the
> argument list against the definition of the method. In S3 one can write
> \usage{\method{generic}{class}} and it would be nice to have an extension
> of this facility for S4 methods. I have been abandoning the skeleton
> structure produced by promptMethods and have been using \section{Usage} and
> \section{Arguments}.

Seems ok to have separate discussion of arguments, but don't "abandon"
the rest of the material in the skeleton (see below).

Heavy use of extra arguments in the methods is a little bit worrisome. 
There is an efficiency penalty, though not likely serious in sizable
computations.  More basic (this is just my personal view), I like to
think of the function as having a single conceptual definition--what it
does and (by and large) what arguments it takes to describe what it
should do.  Then the methods are the implementation.  The function
description is likely what users, begining users particularly, want to
see.  More advanced users and programmers may also be concerned with the
implementation.

So, most of the time, one would like the function to define the
arguments, and the methods to work from these.

In some examples of extra arguments (the S3 print() methods, for
instance), these are style-setting parameters, or perhaps control
parameters for numeric computations.  It might be clearer in such cases
to say that "..." is always passed to a (class-dependant)
parameter-setting function.  Documenting that function is then a
separate step.

Again, this is just by way of what may help users to understand the
functions and help designers to write functions cleanly; not suggesting
you should be forced to take this route.

> 
> 3. The aliases for methods are pretty verbose and make the html contents
> page for the package look rather cluttered. I have been deleting the
> \alias{foo-methods} alias and been replacing \alias{foo,bar1,bar2-method}
> with \alias{foo.bar1.bar2}. I know that using a syntactically valid name
> for the alias has the potential problem that a function could actually
> exist with that name, but I just like to use something shorter.

Don't do that.  It's not what you like that counts, it's what works with
the ? function, and your change will wipe out the ability of the help
functions to identify correctly which method is being documented.

For 1.8 (unfortunately, unlikely to be ironed out for 1.7.1), users
should be able to get documentation on the method, say, for function
f(x,y) corresponding to signature(x = "character", y = "numeric") by the
expression
  method ? f(x="character", y = "numeric")
(or something along these lines).

In any case, the \alias lines are crucial to going from any way of
requesting method documentation to the correct documentation.

> 
> 4. There don't seem to be any guidelines for documenting a method with the
> generic, if the generic happens to be defined in the same package, or with
> the object class, if the generic dispatches on only one argument. I know
> that you have thought about this, and in the document
> http://developer.r-project.org/moreClassMethodIssues.html you refer to the
> 'addTo' argument for 'promptMethods'. The 'addTo' argument however has not
> yet been implemented in R.
> 
> It would be nice to have a method for finding dynamically all available
> documentation for methods for a given generic function. I wrote a little
> prototype function called 'helpMethods' which simply extracts the list of
> available methods and prompts the user for which help topic they'd like to
> read. For this to work though, developers need to use a consistent alias
> system for documenting methods. I haven't seen any package yet which is
> using the aliases suggested by promptMethods.
> 
> Do you think there is any value in my S4 documentation guide? Are there
> errors or mis-understandings in it which should be corrected before it is
> adopted as a guideline by Bioconductor?

It's a useful document to have.  The whole area of documentation and
online help is being worked on by a number of people, so there is the
"moving target" difficulty.

You mention in your document altering the output of the promptMethods
skeleton.  Adding material, up to a point, is OK, but changing or
deleting the "\" lines is not a good idea if you want the documentation
to work with R's (evolving) help system.  As noted, the \alias lines
should be left alone.

There are a few other points we can discuss off-list, not directly
related to this thread.

> 
> Are there major changes planned for the documentation system for S4 methods
> and classes in R in the near future? Is it worth our while spending time
> working out guidelines now or should we wait a bit until the situation
> stabilizes?

Commented on above--yes changes are in prospect.  Bioconductor may want
to encourage documentation even before things settle down--really for
the people in the project to assess whether guidelines are helpful at
this point.

As said, there will be some changes for 1.8, mostly additions to the
code that processes the online help requests. It's a fairly good guess
that the structure of \ lines, esp. the \alias lines, will be kept or
extended, not radically changed, so keeping the current prompt output of
these lines would be desirable.  If there are changes in the structure,
you're more likely to see tools to modify what you have if you follow
the current prompt output.

In the longer run, it would be useful to have a documentation system
based on a more modern form (e.g., XML), making possible more powerful
online help software.  Duncan Temple Lang and others have done some good
work on such systems.  My crystal ball is very foggy on what will happen
with the R community in this direction.

Regards,
 John

> 
> Best wishes
> Gordon
> 
> >Date: Fri, 23 May 2003 15:37:50 -0400
> >From: John Chambers <jmc@research.bell-labs.com>
> >Subject: Re: [Rd] Documenting S4 classes; debugging them
> >To: Duncan Murdoch <dmurdoch@pair.com>
> >Cc: r-devel@stat.math.ethz.ch
> >
> >Duncan Murdoch wrote:
> > >
> > > 1.  I'm putting together my first package that uses S4 classes and
> > > objects.  I'd like to document them, but I'm not sure what the
> > > documentation should look like, and package.skeleton doesn't produce
> > > any at all for the classes or methods.
> >
> >Hmm, sounds as if it should.
> >
> >Meanwhile, promptClass and promptMethods generate skeleton
> >documentation.
> >
> > >
> > > Are there any good examples to follow?
> >
> >The bioconductor packages (e.g, Biobase) have some examples.
> 
> ...
> 
> >John
> >
> > >
> > > Duncan Murdoch
> > >
> > > ______________________________________________
> > > R-devel@stat.math.ethz.ch mailing list
> > > https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
> >
> >--
> >John M. Chambers                  jmc@bell-labs.com
> >Bell Labs, Lucent Technologies    office: (908)582-2681
> >700 Mountain Avenue, Room 2C-282  fax:    (908)582-3340
> >Murray Hill, NJ  07974            web: http://www.cs.bell-labs.com/~jmc
> 
> ---------------------------------------------------------------------------------------
> Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3050, Australia
> Tel: (03) 9345 2326, Fax (03) 9347 0852,
> Email: smyth@wehi.edu.au, www: http://www.statsci.org
> 
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel

-- 
John M. Chambers                  jmc@bell-labs.com
Bell Labs, Lucent Technologies    office: (908)582-2681
700 Mountain Avenue, Room 2C-282  fax:    (908)582-3340
Murray Hill, NJ  07974            web: http://www.cs.bell-labs.com/~jmc


Documenting classes and methods: was [Rd] Re: R-devel Digest, Vol 3, Issue 23
John Chambers