Convert between bibliography formats
Read a bibliography file in one of the supported formats, convert it to nnother format, and write it to a file.
bibConvert(infile, outfile, informat, outformat, ..., tex, encoding,
options)infile |
input file, a character string. |
outfile |
output file, a character string. |
informat |
input format, a character string, see Details. |
outformat |
output format, a character string, see Details. |
... |
not used. |
tex |
TeX specific options, see Details, a character vector. |
encoding |
|
options |
mainly for debugging: additional options for the converters, see Details. |
Arguments informat and outformat can usually be omitted,
since bibConvert infers them from the extensions of the names
of the input and output files, see section "File extensions" below.
However, there is ambiguity for the extension "bib", since it
is used for Bibtex and BibLaTeX entries. For this extension, the
default for both, informat and outformat, is
"bibtex".
Package rbibutils supports format "bibentry", in addition
to the formats supported by the bibutils library. A bibentry
object contains one or more references. Two formats are supported for
"bibentry" for both input and output. A bibentry object
previously saved to a file using saveRDS (default extension
"rds") or an R source file containing one or more
bibentry commands. The "rds" file is just read in and
should contain a bibentry object.
When bibconvert outputs to an R source file, two variants are
supported: "R" and "Rstyle". When (outformat =
"R", there is one bibentry call for each reference, just as in
a Bibtex file, each reference is a single entry. outformat =
"Rstyle" uses the format of print(be, style = "R"), i.e., the
bibentry calls are output as a comma separated sequence wrapped
in c(). For input, it is not necessary to specify which
variant is used.
Note that when the input format and output formats are identical, the
conversion is not necessarilly a null operation (except for
xml, and even that may change). For example, depending on the
arguments the character encoding may change. Also, input BibTeX files
may contain additional instructions, such as journal abbreviations,
which are expanded and incorporated in the references but not
exported. It should be remembered also that there may be loss of
information when converting from one format to another.
For complete list of supported bibliography formats, see section
"Supported input and output formats" in rbibutils and
the documentation of the original bibutils library.
Argument encoding is a character vector containing 2 elements,
specifying the encoding of the input and output files. If the
encodings are the same, a length one vector can be supplied. The
default encodings are UTF-8 for input and output. A large number of
familiar encodings are supported, e.g. "latin1" and
"cp1251" (Windows Cyrillic). Some encodings have two or more
aliases and they are also accepted. If an unknown encoding is
requested, a list of all supported encodings will be printed.
Argument tex is an unnamed character vector containing switches
for bibtex input and output (mostly output). Currently, the following
are available:
write bibtex tags/types in upper case.
do not convert latex-style character combinations to letters.
use brackets, not quotation marks surrounding data.
use one dash "-", not two "--", in page ranges.
add final comma to bibtex output.
By default latex encodings for accented characters are converted to
letters. This may be a problem if the output encoding is not UTF-8,
since some characters created by this process may be invalid in that
encoding. For example, a BibTeX file which otherwise contains only
cyriilic and latin characters may have a few entries with authors
containing latin accented characters represented using the TeX
convention. If those characters are not converted to Unicode letters,
they can be exported to "cp1251" (Windows Cyrillic) for
example. Specifying the option no_latex should solve the
problem in such cases.
Argument options is mostly for debugging and mimics the command
line options of the bibutils' binaries. The argument is a named
character vector and is supplied as c(tag1= val1, tag2 = val2,
...), where each tag is the name of an option and the value is the
corresponding value. The value for options that do not require one is
ignored and can be set to "". Some of the available options
are:
help, show all available options.
do not write Byte Order Mark in UTF8 output.
print intermediate output.
print even more intermediate output.
The function is used for the side effect of creating a file in the requested format. It returns a list, currently containing the following components:
infile |
name of the input file, |
outfile |
name of the output file, |
nref_in |
number of references read from the input file, |
nref_out |
number of references written to the output file. |
If an input or output format is not specified by arguments, it is inferred, if possible, from the file extension. The table below contains the file extension in the in the first column and the corresponding default format in the second.
| ads | ADS reference format |
| bib | BibTeX |
| bibtex | BibTeX |
| biblatex | BibLaTeX |
| copac | COPAC format references |
| end | EndNote (Refer format) |
| endx | EndNote XML |
| isi | ISI web of science |
| med | Pubmed XML references |
| nbib | Pubmed/National Library of Medicine nbib format |
| ris | RIS format |
| R | R source file containing bibentry commands |
| r | R source file containing bibentry commands |
| Rstyle | R source file containing bibentry commands |
| rds | bibentry object in a binary file created by saveRDS() |
| xml | MODS XML intermediate |
| wordbib | Word 2007 bibliography format |
Georgi N. Boshnakov
Chris Putnam, Library bibutils,
https://sourceforge.net/projects/bibutils/.
fn_biblatex <- system.file("bib", "ex0.biblatex", package = "rbibutils")
fn_biblatex
## file.show(fn_biblatex)
## convert a biblatex file to xml
modl <- tempfile(fileext = ".xml")
bibConvert(infile = fn_biblatex, outfile = modl, informat = "biblatex", outformat = "xml")
## file.show(modl)
## convert a biblatex file to bibtex
bib <- tempfile(fileext = ".bib")
bib2 <- tempfile(fileext = ".bib")
bibConvert(infile = fn_biblatex, outfile = bib, informat = "biblatex", outformat = "bib")
## file.show(bib)
## convert a biblatex file to bibentry
rds <- tempfile(fileext = ".rds")
fn_biblatex
rds
be <- bibConvert(fn_biblatex, rds, "biblatex", "bibentry")
bea <- bibConvert(fn_biblatex, rds, "biblatex") # same
readRDS(rds)
## convert to R source file
r <- tempfile(fileext = ".R")
bibConvert(fn_biblatex, r, "biblatex")
## file.show(r)
cat(readLines(r), sep = "\n")
fn_cyr_utf8 <- system.file("bib", "cyr_utf8.bib", package = "rbibutils")
## Can't have files with different encodings in the package, so below
## first convert a UTF-8 file to something else.
##
## input here contains cyrillic (UTF-8) output to Windows Cyrillic,
## notice the "no_latex" option
a <- bibConvert(fn_cyr_utf8, bib, encoding = c("utf8", "cp1251"), tex = "no_latex")
## now take the bib file and convert it to UTF-8
bibConvert(bib, bib2, encoding = c("cp1251", "utf8"))
## Latin-1 example: Author and Title fileds contain Latin-1 accented
## characters, not real names. As above, the file is in UTF-8
fn_latin1_utf8 <- system.file("bib", "latin1accents_utf8.bib", package = "rbibutils")
## convert to Latin-1, by default the accents are converted to TeX combinations:
b <- bibConvert(fn_latin1_utf8, bib , encoding = c("utf8", "latin1"))
cat(readLines(bib), sep = "\n")
## use "no_latex" option to keep them Latin1:
c <- bibConvert(fn_latin1_utf8, bib , encoding = c("utf8", "latin1"), tex = "no_latex")
## this will show properly in Latin-1 locale (or suitable text editor):
##cat(readLines(bib), sep = "\n")
unlink(c(modl, bib, bib2, r, rds))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.