write_bib: Generate BibTeX bibliography databases for R packages

In knitr: A General-Purpose Package for Dynamic Report Generation in R

Generate BibTeX bibliography databases for R packages

Description

This function uses utils::citation() and utils::toBibtex() to create bib entries for R packages and write them in a file. It can facilitate the auto-generation of bibliography databases for R packages, and it is easy to regenerate all the citations after updating R packages.

Usage

write_bib(
  x = .packages(),
  file = "",
  tweak = TRUE,
  width = NULL,
  prefix = getOption("knitr.bib.prefix", "R-"),
  lib.loc = NULL,
  packageURL = TRUE
)

Arguments

x	Package names. Packages which are not installed are ignored.
file	The (‘.bib’) file to write. By default, or if NULL, output is written to the R console.
tweak	Whether to fix some known problems in the citations, especially non-standard format of author names.
width	Width of lines in bibliography entries. If NULL, lines will not be wrapped.
prefix	Prefix string for keys in BibTeX entries; by default, it is ‘⁠R-⁠’ unless option('knitr.bib.prefix') has been set to another string.
lib.loc	A vector of path names of R libraries.
packageURL	Use the URL field from the ‘DESCRIPTION’ file. See Details below.

Details

For a package, the keyword ‘⁠R-pkgname⁠’ is used for its bib item, where ‘⁠pkgname⁠’ is the name of the package. Citation entries specified in the ‘CITATION’ file of the package are also included. The main purpose of this function is to automate the generation of the package citation information because it often changes (e.g. author, year, package version, ...).

There are at least two different uses for the URL in a reference list. You might want to tell users where to go for more information; in that case, use the default packageURL = TRUE, and the first URL listed in the ‘DESCRIPTION’ file will be used. Be careful: some authors don't put the most relevant URL first. Alternatively, you might want to identify exactly which version of the package was used in the document. If it was installed from CRAN or some other repositories, the version number identifies it, and packageURL = FALSE will use the repository URL (as used by utils::citation()).

Value

A list containing the citations. Citations are also written to the file as a side effect.

Note

Some packages on CRAN do not have standard bib entries, which was once reported by Michael Friendly at https://stat.ethz.ch/pipermail/r-devel/2010-November/058977.html. I find this a real pain, and there are no easy solutions except contacting package authors to modify their DESCRIPTION files. Anyway, the argument tweak has provided ugly hacks to deal with packages which are known to be non-standard in terms of the format of citations; tweak = TRUE is by no means intended to hide or modify the original citation information. It is just due to the loose requirements on package authors for the DESCRIPTION file. On one hand, I apologize if it really mangles the information about certain packages; on the other, I strongly recommend package authors to consider the ‘⁠Authors@R⁠’ field (see the manual Writing R Extensions) to make it easier for other people to cite R packages. See knitr:::.tweak.bib for details of tweaks. Also note this is subject to future changes since R packages are being updated. If you want to contribute more tweaks, please edit the file ‘inst/misc/tweak_bib.csv’ in the source package.

Author(s)

Yihui Xie and Michael Friendly

Examples

write_bib(c("RGtk2", "gWidgets"), file = "R-GUI-pkgs.bib")
unlink("R-GUI-pkgs.bib")

write_bib(c("animation", "rgl", "knitr", "ggplot2"))
write_bib(c("base", "parallel", "MASS"))  # base and parallel are identical
write_bib("cluster", prefix = "")  # a empty prefix
write_bib("digest", prefix = "R-pkg-")  # a new prefix
write_bib("digest", tweak = FALSE)  # original version

# what tweak=TRUE does
str(knitr:::.tweak.bib)

knitr documentation built on Sept. 11, 2024, 6:18 p.m.