write_bib {knitr}R Documentation

Generate BibTeX bibliography databases for R packages

Description

This function uses citation and toBibtex to create bib entries for R packages and write them in a file. Only the auto-generated citations are included for a package. This function 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-"))

Arguments

x

package names (packages which are not installed are ignored)

file

the (‘.bib’) file to write (by default writes to the R console; ignored if it is NULL)

tweak

whether to fix some known problems in the citations, especially non-standard format of authors

width

the width of lines in bibliographyb entries (if NULL, lines will not be wrapped)

prefix

a prefix string for keys in BibTeX entries; by default, it is R- unless option('knitr.bib.prefix') has been set to another string

Details

The citation is forced to be generated from the ‘DESCRIPTION’ file of the package (citation(auto = TRUE)). The keyword R-pkgname is used for the bib item, where pkgname is the name of the package. All references specified in the ‘CITATION’ file of the package are ignored. 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, ...). By comparison, paper/book citations don't change too often, so it is not a lot of work even if you just cut and paste such bibliography entries from toBibtex(citation()).

Value

a list containing the citations (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")
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)

[Package knitr version 1.15.20 Index]