What about a bib file

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What about a bib file

Romain François
Hi,

Doing the following command on the freshest R-devel i get 223 entries :

$ grep  "The New S Language" */man/*.Rd | wc -l

Would it make sense to add a bib file (or another format) such that one
could do something like :

\cite{blueBook}

or even :

\cite[base]{blueBook}

What do you think ?

Romain

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Re: What about a bib file

Vincent Carey 525-2265
Romain Francois suggests that a central bibliographic database
(possibly in bibtex format) might be useful for reference inclusion
in R package man pages.  This has been discussed by a small
group, with one proposal presented for a package-specific bibtex database
placed in a dedicated package subdirectory.  Man page references would
then cite the sources enumerated in the database using their bibtex
tags.  This approach could encourage better annotation and should
confer greater accuracy on package:literature referencing.

This does not rule out a central archive that might include all the
references cited in base man pages.

We are doing some work on harvesting the bibliographic citations
in man pages in an R distribution, and converting them to a regular
format.  The \references section is free form, so the conversion
is not trivial, but progress has been made.

The infrastructure required to use this approach to propagate
(e.g., bibtex-formatted) bibliographic data into the man pages that
cite the sources is not yet available, but we hope to have some
prototypes in the next month.

[apologies if i mess up the threading on this topic; i did not receive
the original e-mail to r-devel]

Vince Carey
[hidden email]

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Re: What about a bib file

Martin Maechler
>>>>> "Vince" == Vincent Carey 525-2265 <[hidden email]>
>>>>>     on Mon, 30 Jan 2006 17:49:37 -0500 (EST) writes:

    Vince> Romain Francois suggests that a central bibliographic database
    Vince> (possibly in bibtex format) might be useful for reference inclusion
    Vince> in R package man pages.  This has been discussed by a small
    Vince> group, with one proposal presented for a package-specific bibtex database
    Vince> placed in a dedicated package subdirectory.  Man page references would
    Vince> then cite the sources enumerated in the database using their bibtex
    Vince> tags.  This approach could encourage better annotation and should
    Vince> confer greater accuracy on package:literature referencing.

a very good idea!
I've wished more than once that we had something like that in
place...

My intermediate workaround has been the following, e.g., in
package 'cluster', in man/fanny.Rd,  I have
   \seealso{
     \code{\link{agnes}} for background and references;
     ....
   }

and then no \references{.} in the fanny.Rd file;  but this
workaround is not very satisfactory,
and I am looking forward to your proposals.

Martin Maechler, ETH Zurich


    Vince> This does not rule out a central archive that might include all the
    Vince> references cited in base man pages.

    Vince> We are doing some work on harvesting the bibliographic citations
    Vince> in man pages in an R distribution, and converting them to a regular
    Vince> format.  The \references section is free form, so the conversion
    Vince> is not trivial, but progress has been made.

    Vince> The infrastructure required to use this approach to propagate
    Vince> (e.g., bibtex-formatted) bibliographic data into the man pages that
    Vince> cite the sources is not yet available, but we hope to have some
    Vince> prototypes in the next month.

    Vince> [apologies if i mess up the threading on this topic; i did not receive
    Vince> the original e-mail to r-devel]

    Vince> Vince Carey
    Vince> [hidden email]

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Re: What about a bib file

Friedrich.Leisch
In reply to this post by Vincent Carey 525-2265
>>>>> On Mon, 30 Jan 2006 17:49:37 -0500 (EST),
>>>>> Vincent Carey 525-2265 (VC5) wrote:

  > Romain Francois suggests that a central bibliographic database
  > (possibly in bibtex format) might be useful for reference inclusion
  > in R package man pages.  This has been discussed by a small
  > group, with one proposal presented for a package-specific bibtex database
  > placed in a dedicated package subdirectory.  Man page references would
  > then cite the sources enumerated in the database using their bibtex
  > tags.  This approach could encourage better annotation and should
  > confer greater accuracy on package:literature referencing.

  > This does not rule out a central archive that might include all the
  > references cited in base man pages.

  > We are doing some work on harvesting the bibliographic citations
  > in man pages in an R distribution, and converting them to a regular
  > format.  The \references section is free form, so the conversion
  > is not trivial, but progress has been made.

  > The infrastructure required to use this approach to propagate
  > (e.g., bibtex-formatted) bibliographic data into the man pages that
  > cite the sources is not yet available, but we hope to have some
  > prototypes in the next month.

Sounds great! The "hardest" parts are probably

1) a bibtex parser in R
2) at least one function converting arbitrary bibtex entries to text,
   i.e., the R equivalent of a .bst file.

(I'm only guessing what such a system would involve).

After looking into it when writing the citation() infrastructure I
decided I don't want to do it and went straight to S objects written
by the package author. All those string replacements and possible LaTeX
markup simply looked like too much effort for just 1-2 entries per
package ;-)

But it would be great to have the above functionality in R, of
course, and "all references" in a package are certainly a larger set
then what citation() should report, making the effort worthwhile.

My only wish is that the bibtex parser returns objects compatible to
class "citation" (either the same class or simple coercion). I
modelled the class after bibtex entries anyway, so that shouldn't be a
restriction (I hope). If we need to modify class "citation" to be
accomodate your needs, please let me know.

Once we can suck bibtex files into R it would be trivial to give users
a choice between writing

 CITATION files in the current form (with the benefit of headers and
 footers)

or

 mark certain entries in the PACKAGE.bib file (whatever its name may be)
 that they should be reported by citation().

Best,
Fritz

PS: Of course I volunteer to alpha-test any prototypes you have,

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