Re: [Rd] R package BibTex entries: looking for a more general solution

From: Yihui Xie <xie_at_yihui.name>
Date: Wed, 03 Nov 2010 09:18:15 -0500

I strongly support this proposal! I also find it inconvenient to cite some R packages and really do not like edit the BibTeX entries manually.

Regards,
Yihui

--
Yihui Xie <xieyihui_at_gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA



On Wed, Nov 3, 2010 at 8:44 AM, Michael Friendly <friendly_at_yorku.ca> wrote:

> == Summary ==
> * Problem: BibTeX entries extracted from R packages via citation() require
> too much manual editing to be
> of general use.
> * Proposal: Date: fields should be made mandatory in package DESCRIPTION
> files, perhaps
> beginning with warnings from R CMD check
> * Proposal: Package authors should be encouraged to use a (new)
> Contributors: field in the DESCRIPTION file
> rather than packing all information into the Author: field, which at present
> cannot often be parsed by BibTeX.
> * Files: All test files referred to here can be found at
>
> http://euclid.psych.yorku.ca/SCS/Private/Rbibs/
>
> == Details ==
> Around 16 Dec. 2009, I queried R-help about automating the extraction of
> citation()s from R packages. The stimulus
> was that some journals, notably JSS, now require a reference and citation of
> every R package mentioned,
> and it is a pain to create these manually, no less maintain them for current
> versions.
>

> The result of that query was a function, Rpackage.bibs() by Achim Zeileis
> that I have been using ever since.
> Code in: http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpackages.bib.R
> On one current system I get the following:
>
>> Rpackage.bibs(file="Rpackages-R.2.11.1.bib")
> Converted 230 of 230 package citations to BibTex
> Results written to file Rpackages-R.2.11.1.bib
> Warning messages:
> 1: In citation(x) :
> no date field in DESCRIPTION file of package 'codetools'
> 2: In citation(x) :
> no date field in DESCRIPTION file of package 'gridBase'
> 3: In citation(x) : no date field in DESCRIPTION file of package 'iplots'

>>
> See:
>
http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpkg-test.pdf
> for the result of processing this .bib file with latex/bibtex using the
> jss.bst bibliography style
>
> I'm writing to R-Devel because the DESCRIPTION and inst/CITATION files in R
> packages provide the
> basic data used in citation() and any methods based on this, and yet the
> information in these files is
> often insufficient to generate well-formed BibTeX entries for use in
> vignettes and publications.

>
> One easy case is illustrated above, where 3 packages have no Date: field so
> the BibTeX gets no
> year = {},
> and references get printed as Murrell, P (????) for gridBase. (In my
> original test under R 2.9.1, there where
> ~ 20 such warnings.) Thus, I propose that Date: be a required field in
> DESCRIPTION files, and
> R CMD check complain if this is not found.

>
> The more difficult case has to do with the Author: field in the DESCRIPTION
> file (when no CITATION file is present)
> People can write whatever they want here, and the result looks sort of OK
> when printed by citation(), but confuses
> BibTeX mightly. One example:

>
>> citation("akima")
> To cite package ‘akima’ in publications use:
>
> Fortran code by H. Akima R port by Albrecht Gebhardt aspline function
> by Thomas Petzoldt <petzoldt_at_rcs.urz.tu-dresden.de> enhancements and
> corrections by Martin Maechler (2009). akima: Interpolation of
> irregularly spaced data. R package version 0.5-4.
> http://CRAN.R-project.org/package=akima
>
> A BibTeX entry for LaTeX users is
>
> @Manual{,
> title = {akima: Interpolation of irregularly spaced data},
> author = {Fortran code by H. Akima R port by Albrecht Gebhardt aspline
> function by Thomas Petzoldt <petzoldt_at_rcs.urz.tu-dresden.de> enhancements
> and corrections by Martin Maechler},
> year = {2009},
> note = {R package version 0.5-4},
> url = {http://CRAN.R-project.org/package=akima},
> }
>
> ATTENTION: This citation information has been auto-generated from the
> package DESCRIPTION file and may need manual editing, see
> ‘help("citation")’ .
>>
>
> Yes, the ATTENTION note does say that manual editing may be necessary, but I
> think a worthy goal would be
> to try to reduce the need for this.

>
> One simple way to do that would be to support an extra Contributions: field
> in the DESCRIPTION file,
> so that Authors: can be more cleanly separated for the purpose of creating
> well-structured BibTeX.
> Perhaps others have better ideas.

>
> -Michael
>
> --
> Michael Friendly     Email: friendly AT yorku DOT ca
> Professor, Psychology Dept.
> York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
> 4700 Keele Street    Web:http://www.datavis.ca
> Toronto, ONT  M3J 1P3 CANADA
>
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
______________________________________________ R-devel_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Received on Wed 03 Nov 2010 - 14:23:12 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Wed 03 Nov 2010 - 18:30:15 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-devel. Please read the posting guide before posting to the list.

list of date sections of archive