(xposted to bioc-devel and r-devel as I feel it is relevant to both
communities)

As someone whose body of work is likely to consist mostly of
infrastructural packages and research directly in computing I
wholeheartedly agree with Kasper's suggestion that we as a community should
work to provide and use package citations. I borrow heavily from existing
work in terms of both concept and implementation, and I hope that my ideas
will in turn be borrowed in future work by others in the same way that
science builds on existing results. Just because we write software doesn't
mean we are not doing research.

I think we can actually do more than just citing packages we used when we
write papers about analyses though. Starting with the  packages I will be
releasing as part of my thesis, I intend to include a bibliography file
within each package that includes citations for other packages or
publications that the work is built on or extends (or is similar enough to
otherwise warrant a citation).

Not all packages are ever attached to publications, but in a very real
sense putting a package on CRAN or BioC IS publication, and as Kasper says
it is important for us as a community to give credit where credit is due.
That includes when we write a new package which builds on ideas explored by
existing (or even defunct) packages.

I would love to see this included as an optional but canonical part of the
R package structure, but for now I will simply put it in inst/bib. I humbly
suggest other people consider doing the same.

~G


On Sun, Nov 17, 2013 at 6:31 PM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> Fellow package authors,
>
> I have been reviewing a number of Bioconductor packages for a publication,
> and for that purpose I have been interested in citing numerous packages.
>  For (too many) packages it has been (too) hard to find the relevant
> information.
>
> Let me remind you of the CITATION file and the command
>  R> citation("PKGNAME")
> which allows someone like me to quickly get the relevant citation for the
> package.  See R-extensions.  Sometimes it is complicated (see for example
> limma, where different methods require different citations), and the
> vignette seems to be a good place to put this.  In fact, I would always
> have a citation section in the vignette.
>
> Many of us would like credit for our work in the form of citations; let us
> not make it hard on the user to figure out how to do this.
>
> Best,
> Kasper
>
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>
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>



-- 
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis

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