[Bioc-devel] Citation of an accompanying paper

[Gabe Becker]

Alina,

Typically in cases like the one you describe, people want users to use the
paper citation when citing use of the package. Whether this is what they
"should" want is somewhat debatable, but at least it seems reasonable, as
by using the package users are, assumedly, applying the method your package
implements.

That said, a package can (from a mechanical perspective) have list more
than one citation in it's CITATION file. Xie's knitr does this, for example
(seehttps://github.com/yihui/knitr/blob/master/inst/CITATION and what is
returned from citation(package="knitr") ) .

Whether it's good to do this, and more generally whether package users
should be expected to cite a (theory-based) methods paper and software
which implements the method, particularly when they are by the same author,
is again debatable. I have my thoughts on that but it's somewhat tangential
to your question.

It might be valuable for the Bioconductor team to have guidelines/an
official view of how to navigate these issues.

Best,
~G

On Wed, Mar 22, 2017 at 9:36 AM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:

> If you do not have a CITATION file, a citation is automatically generated.
> So yes, effectively it would overwrite.  See details in R-exts.
>
> On Wed, Mar 22, 2017 at 6:30 AM, Alina Selega <alina.selega at gmail.com>
> wrote:
>
> > Hi Monther,
> >
> > Thank you for your reply!
> >
> > Would that overwrite the package citation that currently shows up on the
> > page though? My paper doesn't cite the Bioconductor package (as it was
> > accepted before I had a valid link to include), it just refers to the
> same
> > name of the computational method. Is there a way to include both
> citations?
> > And if not, which one should I keep?
> >
> > Thanks,
> > Alina
> >
> > On 21 March 2017 at 22:13, Monther Alhamdoosh <m.hamdoosh at gmail.com>
> > wrote:
> >
> > > Hi Alina,
> > >
> > > I think you need to add a file named CITATION in your package (usually
> > > under the inst folder) and use bibentry as follows
> > >
> > > bibentry(bibtype = "Article",
> > >
> > >          title = "Combining multiple tools outperforms individual
> methods
> > > in gene set enrichment analyses",
> > >
> > >          author = c(person("Monther", "Alhamdoosh"),
> > >
> > >                     person("Milica", "Ng"),
> > >
> > >                     person("Nicholas", "Wilson"),
> > >
> > >                     person("Julie", "Sheridan"),
> > >
> > >                     person("Huy", "Huynh"),
> > >
> > >                     person("Michael", "Wilson"),
> > >
> > >                     person("Matthew", "Ritchie")),
> > >
> > >          journal = "Bioinformatics",
> > >
> > >          page = "414-424",
> > >
> > >          volume = 33,
> > >
> > >          number = 3,
> > >
> > >          year = 2017,
> > >
> > >          doi = "10.1093/bioinformatics/btw623")
> > >
> > >
> > >
> > > Cheers,
> > >
> > > Monther
> > >
> > > On Wed, Mar 22, 2017 at 8:11 AM, Alina Selega <alina.selega at gmail.com>
> > > wrote:
> > >
> > >> Hi,
> > >>
> > >> My methods paper (doi:10.1038/nmeth.4068) associated with my package
> > >> BUMHMM
> > >> was accepted before I submitted the package for revision at
> > Bioconductor.
> > >> I
> > >> would like the package page to also hold the citation to the paper.
> What
> > >> is
> > >> the best way to add this paper citation? (I cite it in the vignette,
> but
> > >> it
> > >> would be nice to also have it on the main page.)
> > >>
> > >> Thank you,
> > >> Alina Selega
> > >>
> > >>         [[alternative HTML version deleted]]
> > >>
> > >> _______________________________________________
> > >> Bioc-devel at r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>
> > >
> > >
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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>
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-- 
Gabriel Becker, Ph.D
Associate Scientist
Bioinformatics and Computational Biology
Genentech Research

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