| rbibutils-package {rbibutils} | R Documentation |
Read 'Bibtex' Files and Convert Between Bibliography Formats
Description
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.
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.
Author(s)
Georgi N. Boshnakov (R code and R port of bibutils), Chris Putnam (author of bibutils library)
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/.
See Also
bibConvert for further details and examples