From Ted.Harding at nessie.mcc.ac.uk  Tue Jun 14 11:45:48 2005
From: Ted.Harding at nessie.mcc.ac.uk ( (Ted Harding))
Date: Tue, 14 Jun 2005 10:45:48 +0100 (BST)
Subject: [Rd] Citation for R
In-Reply-To: <1abe3fa905061401066530e563@mail.gmail.com>
Message-ID: <XFMail.050614104548.Ted.Harding@nessie.mcc.ac.uk>

On 14-Jun-05 A.J. Rossini wrote:
> Fritz - 
> 
> That's silly.  As someone pointed out, the issue is with the
> publisher, not the citation.  If R-Core were a generally well-known
> and regarded publishing house such as Springer or Microsoft, it would
> not be a problem.  But it's still a nebulous entity to MANY people,
> and so many people fail to understand this open source stuff.  It's
> seriously discouraged by most journals to cite technical reports, for
> example.  And perhaps, R could be considered more of a long-ish
> technical report than a book?   Though perhaps Peter D. could be
> considered the "editor"?  (these questions are not those that I need
> to ask, obviously!)
> 
> (just yesterday, I was asked by a reasonably intelligent colleague,
> with respect to corporate packaging of R: "So they (corporate
> packagers) just pick some version and package it, right?"  and my
> flabbergasted response was:
> 
> "and so, what the heck do you think they (corporate packagers) do with
> SAS, S-PLUS, and SPSS, and why do you think it's different...?").
> 
> best,
> -tony

Tony is getting admirably and justifiably tetchy! His comment
about the packaging of SAS, S-PLUS and SPSS is delightfully
to the point (and, had I been there at the time, I'd have
bought him a beverage of his choice in appreciation).

And, to extend his comment, where for instance does that leave
WinBUGS (see my previous mail)? Granted, perhaps, that in the
citation


  Spiegelhalter, D. J., Thomas, A. and Best, N. G. (2000)
    WinBUGS Version 1.3 User Manual. Cambridge: Medical Research
    Council Biostatistics Unit.
    (Available from www.mrc-bsu.cam.ac.uk/bugs.)


one has a prestigious institute (MRC-BSU) as the publisher.
But, basically, it's the same self-justifiying ordinance all
over again: the creators of the software produce their own
User Manual and "publish" it. The publisher of S-PLUS and its
documentation is "Insightful Corporation": beyond their
achievement in developing S-PLUS, whence their prestige?
(Granted, again, if you look inside the books, you can find
famous names listed as contributors; but we at R can claim
many of these same names ... ).

The issue of "peer review" of software citations has been
raised. Where is the peer review of the S-PLUS or SAS or
SPSS User Manual? OK, the thing that needs peer review is
the software itself. In the "Review" section of journals
you can find critical reviews of software. But these are
not referee'd and usually represent the writer's own views;
furthermore, such reviews are not often cited in articles
where the software has been used to obtain the results in
the article. People just use the stuff, and cite the User
Manual or the "corporate packager".

Also, from time to time you come across published referee'd
articles which analyse the performance of software for
particular purposes, or compare different software packages
for a given purpose. These could be viewed as peer review,
but, again, are rarely cited by the simple user.

Moreover, suppose that citing User Manual or corporate packager
is considered to justify the use of the software in an article.
I have seen many articles where such-and-such software was used
(I mention no names) and "cited" in these terms, where it is
known to discerning users that the software does not correctly
address the tasks it claims to work for, or gives incorrect
results. Yet the "citation box" had been duly ticked, and the
article has successfully gone through the editorial process.
This is not peer review either -- and could only come close to
it if the journal editors' panel of referees could be assumed
sufficiently knowledgeable to be discriminating about such things.

But in that case you don't really need a citation: the referee
says "Used [e.g.] S-PLUS, yes, that's fine for this job and
I could reproduce the analysis using that software and trust
the results. Passed." And such a referee could say exactly
the same for R.

The true peer review of software is done by discriminating
users of the software. Peer review of R is done *HERE* (as
well as other places).

[I've had the experience of using R for analysis, only to
have the analysis repeated in S-PLUS purely for the purpose
of citing S-PLUS rather than R for publication ... ]

However, the follow-ups in this thread are departing somewhat
from Gordon Smyth's original wish to pay tribute, in citation,
to the growing team of people who have, over the last 10+ years,
contributed centrally to making R what it is.

Thinking about that question, I can't come up with a better
idea than his: an up-to-date "Ihaka and Gentleman", which
does due honour to the greatly enhanced riches of R, and R's
solidity and quality, at the present time!

But maybe this might take a book ...

Best wishes to all,
Ted.


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Date: 14-Jun-05                                       Time: 10:45:39
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[Rd] Citation for R
 (Ted Harding