For one point of evidence about how much people pay attention to the
documentation about what's outdated: Brian Ripley added a comment to
nlminb.Rd in 2013 saying that the function was "for historical
compatibility"
<https://github.com/wch/r-source/commit/fd50cf2047b636e496551bcefd6bfa505f93f168>
but it's still widely used in new code ...
But I agree that adding appropriate warnings/links to the
documentation couldn't hurt.
cheers
Ben
On 2023-03-26 12:41 p.m., Duncan Murdoch wrote:
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matter that some tools in the base R distribution are outdated, but that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
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Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
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