[R-pkg-devel] multiple bibentry()s in CITATION
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Mon Mar 27 18:20:00 CEST 2017
I apologize for not being clear. The printing of header depends on the
output style. Indeed text works, but say
print(citation("minfi"), style = "HTML")
does not. Btw., I agree it might be nice to control the printing of header.
On Mon, Mar 27, 2017 at 9:07 AM, Achim Zeileis <Achim.Zeileis at uibk.ac.at>
wrote:
> On Mon, 27 Mar 2017, Kasper Daniel Hansen wrote:
>
> Thanks. It would be great to have this working in 3.4. In Bioc there are
>> multiple packages with CITATION files with multiple entries, one such
>> example is minfi
>> bioconductor.org/packages/minfi
>>
>> On my wishlist is that it would be great to have support for printing the
>> header field which many people use to give a context for the citation. This
>> is important because when you list multiple papers you need (I think) some
>> explanation for when to cite the different ones.
>>
>
> But this is what citation("pkg_name") or print(bibentry_object, style =
> "citation") already do or am I missing something.
>
> I haven't installed "minfi" but just sourced the CITATION into an object x
> and the print(x, style = "citation") seemed to work as intended.
>
> But this is probably a good example where even adding four BibTeX items
> leads to scrolling even on console windows with many lines and columns. In
> these cases it would likely be better not to display any BibTeX and rather
> add a hint as to how the BibTeX can be obtained if desired. In addition to
> Martin's idea with 'citation(package="pkg", bibtex.max=Inf)' one could also
> use 'toBibtex(citation("pkg"))'. The latter, of course, only gives the
> BibTeX but again for long lists like the one in minfi it is probably more
> digestable in separate chunks...
>
> Best,
> Z
>
> Best,
>> Kasper
>>
>> On Mon, Mar 27, 2017 at 7:25 AM, Martin Maechler <
>> maechler at stat.math.ethz.ch
>>
>>> wrote:
>>>
>>
>> Fox, John <jfox at mcmaster.ca>
>>>>>>>> on Mon, 16 Jan 2017 15:44:05 +0000 writes:
>>>>>>>>
>>>>>>>
>>> > Dear Martin,
>>> > Thanks for addressing this question, if belatedly!
>>>
>>> > After a little bit of thought, perhaps a default somewhere between 1
>>> and Inf makes sense, along with an additional argument to citation:
>>> citation(package="pkg", bibtex.max=n), with default bibtex.max=
>>> getOption("citation.bibtex.max"), where the citation.bibtex.max option
>>> is
>>> initially set to something like 4. If the number of available citations
>>> exceeds bibtex.max, then a message like "there are additional BiBTeX
>>> citations, enter 'citation(package="pkg", bibtex.max=Inf)' to see all of
>>> them."
>>>
>>> In the mean time, I have always used my proposed change.
>>> I think any number between 1 and Inf is so much arbitrary that
>>> inspite of your good thoughts I kept the *new* default at Inf.
>>>
>>> and because of this open question, I have forgotten to commit
>>> the change to the development version of R !
>>>
>>> I have done so now, however not ported it yet to "R 3.4.0 alpha".
>>> If not much surfaces (in CRAN / Bioc checks), we may port it in
>>> time for 3.4.0.
>>>
>>>
>>> Martin
>>>
>>> > Best,
>>> > John
>>>
>>> >> -----Original Message-----
>>> >> From: Martin Maechler [mailto:maechler at stat.math.ethz.ch]
>>> >> Sent: Monday, January 16, 2017 10:02 AM
>>> >> To: Fox, John <jfox at mcmaster.ca>
>>> >> Cc: r-package-devel at r-project.org
>>> >> Subject: Re: [R-pkg-devel] multiple bibentry()s in CITATION
>>> >>
>>> >>>>>>> Fox, John <jfox at mcmaster.ca>
>>> >>>>>>> on Fri, 2 Sep 2016 15:42:46 +0000 writes:
>>> >>
>>> >> (which is more than 4 months ago)
>>> >>
>>> >>> Dear list members,
>>> >>> I've noticed that citation(package="pkg") generates both a text
>>> >> citation and a BiBTeX entry when the CITATION file contains a
>>> single
>>> >> call to bibentry() or citEntry(), but that only text citations are
>>> shown
>>> >> if there are multiple calls to bibentry() or citEntry().
>>> >>
>>> >>> Is this behaviour intentional? In my opinion, it's useful always
>>> >> to show the BiBTeX (although it's available through
>>> >> toBibtex(citation(package="pkg")) ).
>>> >>
>>> >>> The Writing R Extensions manual says, "A CITATION file will
>>> >> contain *calls* [my emphasis] to function bibentry."
>>> >>
>>> >>> Thanks,
>>> >>> John
>>> >>
>>> >> and you did not get a reply....
>>> >> I had wanted but forgotten about it ... two parts :
>>> >>
>>> >> 1) On November 24, 2012, I had improved R with an option to get
>>> this
>>> >> so this has been a "hidden gem" ;-) for a while in R:
>>> >>
>>> >>> options(citation.bibtex.max = Inf)
>>> >>> citation(package = "Rcmdr")
>>> >>
>>> >> To cite the 'Rcmdr' package in publications use:
>>> >>
>>> >> Fox, J., and Bouchet-Valat, M. (2017). Rcmdr: R Commander. R
>>> package
>>> >> version 2.3-2.
>>> >>
>>> >> A BibTeX entry for LaTeX users is
>>> >>
>>> >> @Manual{,
>>> >> title = {{Rcmdr: R Commander}},
>>> >> author = {John Fox and Milan Bouchet-Valat},
>>> >> year = {2017},
>>> >> note = {R package version 2.3-2},
>>> >> url = {http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr/},
>>> >> }
>>> >>
>>> >> Fox, J. (2017). Using the R Commander: A Point-and-Click Interface
>>> or
>>> >> R. Boca Raton FL:
>>> >> Chapman and Hall/CRC Press.
>>> >>
>>> >> A BibTeX entry for LaTeX users is
>>> >>
>>> >> @Book{,
>>> >> title = {Using the {R Commander}: A Point-and-Click Interface for
>>> >> {R}},
>>> >> author = {John Fox},
>>> >> year = {2017},
>>> >> publisher = {Chapman and Hall/CRC Press},
>>> >> address = {Boca Raton {FL}},
>>> >> url = {http://socserv.mcmaster.ca/jfox/Books/RCommander/},
>>> >> }
>>> >>
>>> >> Fox, J. (2005). The R Commander: A Basic Statistics Graphical User
>>> >> Interface to R.
>>> >> Journal of Statistical Software, 14(9): 1--42.
>>> >>
>>> >> A BibTeX entry for LaTeX users is
>>> >>
>>> >> @Article{,
>>> >> title = {The {R} {C}ommander: A Basic Statistics Graphical User
>>> >> Interface to {R}},
>>> >> author = {John Fox},
>>> >> year = {2005},
>>> >> journal = {Journal of Statistical Software},
>>> >> volume = {14},
>>> >> number = {9},
>>> >> pages = {1--42},
>>> >> url = {http://www.jstatsoft.org/v14/i09},
>>> >> }
>>> >>
>>> >>>
>>> >> ----------------
>>> >>
>>> >> This all works "obviously" (;-) via utils:::format.bibentry () and
>>> even
>>> >> when I had made the number one an argument to that function with a
>>> >> default you can set via options(), I had wondered a bit why the
>>> cutoff
>>> >> should by default be at one.
>>> >>
>>> >> E.g., it looks strange that by *adding* a 2nd reference, you get
>>> shorter
>>> >> citation output.... and to me it would seem more coherent to have
>>> the
>>> >> default rather be 'Inf' instead of '1', i.e. always showing both
>>> text
>>> >> and bibtex.
>>> >>
>>> >> There is quite a difference though: For our copula package, e.g.,
>>> >>
>>> >>> options(citation.bibtex.max = 1); citation(package = "copula")
>>> >>
>>> >> To cite the R package copula in publications use:
>>> >>
>>> >> Marius Hofert, Ivan Kojadinovic, Martin Maechler and Jun Yan
>>> (2017).
>>> >> copula:
>>> >> Multivariate Dependence with Copulas. R package version 0.999-16
>>> URL
>>> >> https://CRAN.R-project.org/package=copula
>>> >>
>>> >> Jun Yan (2007). Enjoy the Joy of Copulas: With a Package copula.
>>> >> Journal of Statistical
>>> >> Software, 21(4), 1-21. URLhttp://www.jstatsoft.org/v21/i04/.
>>> >>
>>> >> Ivan Kojadinovic, Jun Yan (2010). Modeling Multivariate
>>> Distributions
>>> >> with Continuous
>>> >> Margins Using the copula R Package. Journal of Statistical
>>> Software,
>>> >> 34(9), 1-20. URL
>>> >> http://www.jstatsoft.org/v34/i09/.
>>> >>
>>> >> Marius Hofert, Martin Maechler (2011). Nested Archimedean Copulas
>>> Meet
>>> >> R: The nacopula
>>> >> Package. Journal of Statistical Software, 39(9), 1-20. URL
>>> >> http://www.jstatsoft.org/v39/i09/.
>>> >>
>>> >>>
>>> >>
>>> >> This is relatively compact (18 lines)
>>> >> whereas it gives 67 lines of output when the option is set to
>>> something
>>> >>>= 4.
>>> >>
>>> >> Other opinions?
>>> >> What do you think, would it be worth the compatibility break to
>>> change
>>> >> the default from '1' to 'Inf' ?
>>> >>
>>> >> Best regards,
>>> >> Martin
>>>
>>> ______________________________________________
>>> R-package-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
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