Read 'Bibtex' Files and Convert Between Bibliography Formats

Read and write 'Bibtex' files. Convert between bibliography formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam <https://sourceforge.net/projects/bibutils/>. Supports all bibliography formats and character encodings implemented in 'bibutils'.

Details

Package rbibutils provides an R port of the bibutils programs plus additional facilities. The main function, bibConvert, offers all conversions between bibliography formats supported by library bibutils. In addition, package rbibutils converts to and from R's bibentry Bibtex-based bibliography format.

The core functionality is provided by the bibutils programs which convert between various bibliography formats using a common MODS XML intermediate format, see the source cited below.

Currently we provide the function bibConvert for conversion between supported bibliography formats. For complete list of formats supported by the package, see the documentation of the original bibutils library.

readBib and writeBib import/export BiBTeX files. readBibentry and writeBibentry import/export R source files in which the references are represented by bibentry() calls. These functions were originally just wrappers around bibConvert. readBib has acquired additional features, including a direct import (without going through bibConvert) from BiBTeX files.

All encodings supported by the bibutils library are available for bibConvert.

Further functionality may be provided in future releases, in particular, the underlying C functions could be exposed to package authors. Further R wrappers may be added, as well. However, the scope of the package will remain conversion between formats based on bibutils and manipulation of the MODS XML intermediate format. rbibutils can be used also as an alternative to package bibtex (Francois 2020). For bibliography management see package RefManager (McLean 2017). For citations in R documentation (Rd or roxygen2) see package Rdpack (Boshnakov 2020).

Supported input and output formats

Most formats are supported for both input and output, see the listings below. A format supported for input can be converted to any of the output formats.

The input is first converted to MODS XML intermediate, the latter is then converted to the requested output format. In rbibutils there are currently two exceptions to this rule. First, the conversion from bibtex to bibentry offers the option to bypass the conversion to MODS XML intermediate and parse directly the bibtex file, see readBib for details. Second, the conversion from bibentry to BibTeX just uses a print method provided by R.

In the table below column Abbreviation shows the abbreviation for arguments informat and outformat, column FileExt gives the default file extension for that format, column Input (Output) contains TRUE if the format is supported for input (output) and FALSE otherwise. Column Description gives basic description of the format.

Abbreviation	FileExt	Input	Output	Description
ads	ads	FALSE	TRUE	ADS reference format
bib	bib	TRUE	TRUE	BibTeX
bibtex	bibtex	TRUE	TRUE	BibTeX
biblatex	biblatex	TRUE	TRUE	BibLaTeX
copac	copac	TRUE	FALSE	COPAC format references
ebi	ebi	TRUE	FALSE	EBI XML
end	end	TRUE	TRUE	EndNote (Refer format)
endx	endx	TRUE	FALSE	EndNote XML
isi	isi	TRUE	TRUE	ISI web of science
med	med	TRUE	FALSE	Pubmed XML references
nbib	nbib	TRUE	TRUE	Pubmed/National Library of Medicine nbib format
ris	ris	TRUE	TRUE	RIS format
R, r, Rstyle	R	TRUE	TRUE	R source file containing bibentry commands
rds	rds	TRUE	TRUE	bibentry object in a binary file created by saveRDS()
xml	xml	TRUE	TRUE	MODS XML intermediate
wordbib	wordbib	TRUE	TRUE	Word 2007 bibliography format

bibentry is the native R variant of BibTeX. It can be input directly from an R source file or from a binary rds file. The "rds" format is a compressed binary format. The rds file should contain a bibentry R object, saved from R with saveRDS. An R source file should contain one or more bibentry instructions, see readBibentry for details of the contents.

A bibentry object can be written to a file as a binary ("rds") object or as an R source file, see bibConvert and writeBib for details.

ADS is the reference format of the Smithsonian Astrophysical Observatory (SAO) and National Aeronautics and Space Administration (NASA) Astrophyics Data System.

For COPAC, see https://en.wikipedia.org/wiki/Copac.

Author

Georgi N. Boshnakov (R code and R port of bibutils), Chris Putnam (author of bibutils library)

Note

The bibutils library is included in a number of software packages. These include include pandoc and a library for Haskell. Executable programs for conversion are available for Linux distributions but seem not easily available for Windows. Executable and libraries can also be generated out-of-the-box from the bibutils disribution (on Windows under MSYS).

rbibutils adds conversions to/from R's bibentry format and direct conversion from bibtex, which preserves non-standard fields from the bibtex source. There is also improved support for mathematical expressions in bibtex files.

References

Georgi N Boshnakov (2020). “Rdpack: Update and Manipulate Rd Documentation Objects.” doi:10.5281/zenodo.3925612 , R package version 2.0.0.

Damiano Fantini (2019). “easyPubMed: Search and Retrieve Scientific Publication Records from PubMed.” R package version 2.13, https://CRAN.R-project.org/package=easyPubMed.

Romain Francois (2014). bibtex: bibtex parser. R package version 0.4.0.

Mathew William McLean (2017). “RefManageR: Import and Manage BibTeX and BibLaTeX References in R.” The Journal of Open Source Software. doi:10.21105/joss.00338 .

Chris Putnam (2020). “Library bibutils, version 6.10.” https://sourceforge.net/projects/bibutils/.