[R-pkg-devel] multiple bibentry()s in CITATION

Fox, John jfox at mcmaster.ca
Mon Mar 27 17:12:30 CEST 2017


Dear Martin,

Thanks for following up on this.

Best,
 John

> -----Original Message-----
> From: Martin Maechler [mailto:maechler at stat.math.ethz.ch]
> Sent: March 27, 2017 9:26 AM
> To: Fox, John <jfox at mcmaster.ca>
> Cc: Martin Maechler <maechler at stat.math.ethz.ch>; r-package-devel at r-
> project.org
> Subject: RE: [R-pkg-devel] multiple bibentry()s in CITATION
> 
> >>>>> 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



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