How to cite R packages when using Mendeley?

Question

In Mendeley, the closest category for an R package appears to be "Computer Program"; however, R itself is a computer program, not its packages.

Other literature sources seem to cite technical documents about R packages instead of the actual packages.

Aside from manually entering the citations, is there a way to incorporate R packages in my Mendeley library?

Answer 1

Each R package has a different way to be cited. Some were formally published as scientific articles in journals, some only as packages. The only way to know for sure is to check how the package maintainer want you to cite their package, with function citation. Base R also comes with function toBibtex that help you export the correct citations as a bibtex file.

For instance:

> citation("Rcpp")

To cite Rcpp in publications use:

  Dirk Eddelbuettel and Romain Francois (2011). Rcpp: Seamless
  R and C++ Integration. Journal of Statistical Software,
  40(8), 1-18. URL http://www.jstatsoft.org/v40/i08/.

  Eddelbuettel, Dirk (2013) Seamless R and C++ Integration with
  Rcpp. Springer, New York. ISBN 978-1-4614-6867-7.

  Dirk Eddelbuettel and James Joseph Balamuta (2017). Extending
  R with C++: A Brief Introduction to Rcpp. PeerJ Preprints
  5:e3188v1. URL
  https://doi.org/10.7287/peerj.preprints.3188v1.

To see these entries in BibTeX format, use 'print(<citation>,
bibtex=TRUE)', 'toBibtex(.)', or set
'options(citation.bibtex.max=999)'.

> toBibtex(citation("knitr"))
@Manual{,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2018},
  note = {R package version 1.20},
  url = {https://yihui.name/knitr/},
}

@Book{,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {https://yihui.name/knitr/},
}

@InCollection{,
  booktitle = {Implementing Reproducible Computational Research},
  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  year = {2014},
  note = {ISBN 978-1466561595},
  url = {http://www.crcpress.com/product/isbn/9781466561595},
}

As for importing bibtex files into Mendeley, I do not use Mendeley myself but this Q&A on TeX.se shows that one can simply use menu items "File > Import... > Bibtex (*.bib) " to do so.

Answer 2

You could export the citation as a bibtex file, e.g. https://www.rforge.net/doc/packages/knitr/write_bib.html

Answer 3

With the bibtex package, you can generate a Bibtex file from the package citations and then upload it in Mendeley or another reference manager software. As an example

library(bibtex)
write.bib('package name - here', file='name for the file')
write.bib(c('bibtex', 'utils', 'tools'), file='references') ## for multiple packages

Please see the package's cran page (https://cran.r-project.org/web/packages/bibtex/) for further information

Answer 4

To add to the accepted answer, I believe you are looking for:

writeLines(toBibtex(citation("package")), con = 'path_to/reference_filename')

You can omit the package name for citing R.
Hope it saves someone a few minutes.

Answer 5

knitr::write_bib(c(.packages()), "packages.bib")

This will generate a .bib file containing all used packages, which you can add to Mendeley.

https://bookdown.org/yihui/rmarkdown-cookbook/write-bib.html

Answer 6

For example, if I want to cite Data in Function reference http://ggplot2.tidyverse.org/reference/#section-data, in this case, I will use web page to added to Mendeley manually as follow:

• title = Data - Function reference - ggplot2

• url = http://ggplot2.tidyverse.org/reference/#section-data

• Date access = 2018-02-12