https://github.com/geobosh/rbibutils
Convert bibliography files between various formats, including BibTeX, BibLaTeX, PubMed, RIS, and Bibentry. This is an R port of the bibutils utilities plus R manipulation of bibiliography objects.
https://github.com/geobosh/rbibutils
biblatex bibliography bibtex bibutils conversion endnote pubmed r r-package ris-format
Last synced: 6 months ago
JSON representation
Convert bibliography files between various formats, including BibTeX, BibLaTeX, PubMed, RIS, and Bibentry. This is an R port of the bibutils utilities plus R manipulation of bibiliography objects.
- Host: GitHub
- URL: https://github.com/geobosh/rbibutils
- Owner: GeoBosh
- Created: 2020-05-10T13:43:14.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2023-10-25T14:12:28.000Z (almost 2 years ago)
- Last Synced: 2024-05-09T22:18:13.748Z (over 1 year ago)
- Topics: biblatex, bibliography, bibtex, bibutils, conversion, endnote, pubmed, r, r-package, ris-format
- Language: C
- Homepage: https://geobosh.github.io/rbibutils/
- Size: 2.38 MB
- Stars: 8
- Watchers: 1
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
Awesome Lists containing this project
README
[](https://cran.r-project.org/package=rbibutils)
[](https://www.r-pkg.org/pkg/rbibutils)
[](https://r-pkg.org/pkg/rbibutils)
[](https://github.com/GeoBosh/rbibutils/actions)
[](https://app.codecov.io/gh/GeoBosh/rbibutils)
Read and write 'BibTeX' files. Convert bibliography files between various
formats, including BibTeX, BibLaTeX, PubMed, EndNote and Bibentry. Includes an R
port of the `bibutils` utilities.
# Installing rbibutils
Install the [latest stable version](https://cran.r-project.org/package=rbibutils) from CRAN:
install.packages("rbibutils")
You can also install the [development version](https://github.com/GeoBosh/rbibutils) of `rbibutils` from Github:
library(devtools)
install_github("GeoBosh/rbibutils")
# Overview
Import and export 'BibTeX' files. Convert bibliography files between various
formats. All formats supported by the `bibutils` utilities are available, see
`bibConvert()` for a complete list. In addition, conversion from and to
`bibentry`, the R native representation based on Bibtex, is supported.
`readBib()` and `writeBib()` import/export BiBTeX files. `readBibentry()` and
`writeBibentry()` import/export `R` source files in which the references are
represented by `bibentry()` calls.
The convenience function `charToBib()` takes input from a character vector,
rather than a file. It calls `readBib()` or `bibConvert()`.
`bibConvert()` takes an input bibliography file in one of the supported formats,
converts its contents to another format, and writes the result to a file. All
formats, except for `rds` (see below) are plain text files. `bibConvert()` tries
to infer the input/output formats from the file extentions. There is ambiguity
however about `bib` files, which can be either Bibtex or Biblatex. Bibtex is
assumed if the format is not specified. Also, the `xml` extension is shared by
XML-based formats. Its default is 'XML MODS intermediate' format.
The default encoding is UTF-8 for both, input and output. All encodings handled
by `bibutils` are supported. Besides UTF-8, these include `gb18030` (Chinese),
ISO encodings such as `iso8859_1`, Windows code pages (e.g. `cp1251` for Windows
Cyrillic) and many others. Common alternative names are also accepted
(e.g. `latin1`).
Bibentry objects can be input from an `R` source file or from an `rds` file. The
`rds` file should contain a `bibentry` R object, saved from R with `saveRDS()`.
The `rds` format is a compressed binary format`. Alternatively, an R source file
containing one or more bibentry instructions and maybe other commands can be
used. The R file is sourced and all bibentry objects created by it are
collected.
# Examples:
## readBib
The examples in this section import the following file:
bibacc <- system.file("bib/latin1accents_utf8.bib", package = "rbibutils")
Note that some characters may not be displayed on some locales. Also, on Windows
some characters may be "approximated" by other characters.
Import the above bibtex file into a `bibentry` object. By default TeX escape
sequences representing characters are kept as is:
be0 <- readBib(bibacc)
be0
print(be0, style = "bibtex")
As above, using the direct option:
be1 <- readBib(bibacc, direct = TRUE)
## readBib(bibacc, direct = TRUE, texChars = "keep") # same
be1
print(be1, style = "bibtex")
Use the `"convert"` option to convert TeX sequences to true characters:
be2 <- readBib(bibacc, direct = TRUE, texChars = "convert")
be2
print(be2, style = "R")
(On Windows the Greek characters alpha and delta may be printed as 'a' and 'd'
but internally they are alpha and delta.)
Use the `"export"` option to convert other characters to ASCII TeX sequences,
when possible (currently this option doesn't handle well mathematical
expressions):
be3 <- readBib(bibacc, direct = TRUE, texChars = "export")
print(be3, style = "bibtex")
## bibConvert
Convert Bibtex file `myfile.bib` to a `bibentry` object and save the latter to
`"myfile.rds":
bibConvert("myfile.bib", "myfile.rds", informat = "bibtex", outformat = "bibentry")
bibConvert("myfile.bib", "myfile.rds")
Convert Bibtex file `myfile.bib` to a Biblatex save to `"biblatex.bib":
bibConvert("myfile.bib", "biblatex.bib", "bibtex", "biblatex")
bibConvert("myfile.bib", "biblatex.bib", outfile = "biblatex")
Convert Bibtex file `myfile.bib` to Bibentry and save as `rds` or `R`:
bibConvert("myfile.bib", "myfile.rds")
bibConvert("myfile.bib", "myfile.R")
Read back the above files and/or convert them to other formats:
readLines("myfile.R")
file.show("myfile.R")
readRDS("myfile.rds")
bibConvert("myfile.rds", "myfile.bib")
bibConvert("myfile.R", "myfile.bib")
Assuming `myfile.bib` is a Biblatex file, convert it to Bibtex and save to `bibtex.bib`:
bibConvert("myfile.bib", "bibtex.bib", "biblatex", "bibtex")
bibConvert("myfile.bib", "bibtex.bib", "biblatex")
Assuming "myfile.med" is a PubMed file, convert it to Bibtex:
bibConvert(infile = "myfile.med", outfile = "bibtex.bib", informat = "med", outformat = "bib")
bibConvert(infile = "myfile.med", outfile = "bibtex.bib", informat = "med") # same
See `bibConvert()` for further examples and their results.