[Rd] Query: Could documentation include modernized references?

[Duncan Murdoch]

On 26/03/2023 11:54 a.m., J C Nash wrote:
> A tangential email discussion with Simon U. has highlighted a long-standing
> matter that some tools in the base R distribution are outdated, but that
> so many examples and other tools may use them that they cannot be deprecated.
> 
> The examples that I am most familiar with concern optimization and nonlinear
> least squares, but other workers will surely be able to suggest cases elsewhere.
> I was the source (in Pascal) of Nelder-Mead, BFGS and CG algorithms in optim().
> BFGS is still mostly competitive, and Nelder-Mead is useful for initial exploration
> of an optimization problem, but CG was never very good, right from the mid-1970s
> well before it was interfaced to R. By contrast Rcgmin works rather well
> considering how similar it is in nature to CG. Yet I continue to see use and
> even recommendations of these tools in inappropriate circumstances.
> 
> Given that it would break too many other packages and examples to drop the
> existing tools, should we at least add short notes in the man (.Rd) pages?
> I'm thinking of something like
> 
>      optim() has methods that are dated. Users are urged to consider suggestions
>      from ...
> 
> and point to references and/or an appropriate Task View, which could, of course,
> be in the references.
> 
> I have no idea what steps are needed to make such edits to the man pages. Would
> R-core need to be directly involved, or could one or two trusted R developers
> be given privileges to seek advice on and implement such modest documentation
> additions?  FWIW, I'm willing to participate in such an effort, which I believe
> would help users to use appropriate and up-to-date tools.

I can answer your final paragraph:

Currently R-core would need to be directly involved, in that they are 
the only ones with write permission on the R sources.

However, they don't need to do the work, they just need to approve of it 
and commit it.  So I would suggest one way forward is the following:

- You fork one of the mirrors of the R sources from Github, and (perhaps 
with help from others) edit one or two of the pages in the way you're 
describing.  Once you think they are ready, make them available online 
for others to review (Github or Gitlab would help doing this), and then 
submit the changes as a patch against the svn sources on the R Bugzilla 
site.

- Another way could be that you copy the help page sources to a dummy 
package, instead of checking out the whole of the R sources.  You'll 
need to be careful not to miss other changes to the originals between 
the time you make your copy and the time you submit the patches.

Don't do too many pages, because you're probably going to have to work 
out the details of the workflow as you go, and earn R Core's trust by 
submitting good changes and responding to their requests.  And maybe 
don't do any until you hear from a member of R Core that they're willing 
to participate in this, because they certainly don't accept all suggestions.

Duncan Murdoch