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

2017-03-27 Thread Kasper Daniel Hansen 
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 
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 <
>> maech...@stat.math.ethz.ch
>>
>>> wrote:
>>>
>>
>> Fox, John 
 on Mon, 16 Jan 2017 15:44:05 + 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:maech...@stat.math.ethz.ch]
>>>>> Sent: Monday, January 16, 2017 10:02 AM
>>>>> To: Fox, John 
>>>>> Cc: r-package-devel@r-project.org
>>>>> Subject: Re: [R-pkg-devel] multiple bibentry()s in CITATION
>>>>>
>>>>>> Fox, John 
>>>>>> on Fri, 2 Sep 2016 15:42:46 + 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 =

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

2017-03-27 Thread Fox, John 
Dear Martin,

Thanks for following up on this.

Best,
 John

> -Original Message-
> From: Martin Maechler [mailto:maech...@stat.math.ethz.ch]
> Sent: March 27, 2017 9:26 AM
> To: Fox, John 
> Cc: Martin Maechler ; r-package-devel@r-
> project.org
> Subject: RE: [R-pkg-devel] multiple bibentry()s in CITATION
> 
> > Fox, John 
> > on Mon, 16 Jan 2017 15:44:05 + 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:maech...@stat.math.ethz.ch]
> >> Sent: Monday, January 16, 2017 10:02 AM
> >> To: Fox, John 
> >> Cc: r-package-devel@r-project.org
> >> Subject: Re: [R-pkg-devel] multiple bibentry()s in CITATION
> >>
> >> > Fox, John 
> >> > on Fri, 2 Sep 2016 15:42:46 + 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

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

2017-03-27 Thread Kasper Daniel Hansen 
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.

Best,
Kasper

On Mon, Mar 27, 2017 at 7:25 AM, Martin Maechler  wrote:

> > Fox, John 
> > on Mon, 16 Jan 2017 15:44:05 + 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:maech...@stat.math.ethz.ch]
> >> Sent: Monday, January 16, 2017 10:02 AM
> >> To: Fox, John 
> >> Cc: r-package-devel@r-project.org
> >> Subject: Re: [R-pkg-devel] multiple bibentry()s in CITATION
> >>
> >> > Fox, John 
> >> > on Fri, 2 Sep 2016 15:42:46 + 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},
> >> }
> >>
> >> >
> >>

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

2017-03-27 Thread Martin Maechler 
> Fox, John 
> on Mon, 16 Jan 2017 15:44:05 + 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:maech...@stat.math.ethz.ch]
>> Sent: Monday, January 16, 2017 10:02 AM
>> To: Fox, John 
>> Cc: r-package-devel@r-project.org
>> Subject: Re: [R-pkg-devel] multiple bibentry()s in CITATION
>> 
>> > Fox, John 
>> > on Fri, 2 Sep 2016 15:42:46 + 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:
>> 
>>