Read and write bibtex files
readBib.RdRead and write bibtex files.
Arguments
- file
name or path to the file, a character string.
- encoding
the encoding of
file, a character string.- direct
If
TRUEparse 'file' directly tobibentry, otherwise convert first to intermediate XML, then tobibentry.- texChars
-
What to do with characters represented by TeX commands (for example, accented Latin charaters? If
"export", export as TeX escapes when possible. If"convert", convert to the target encoding. If"keep", output the characters as they were in the input file, like"export", but don't convert normal characters to TeX escapes."Rdpack"is mainly for internal use and its actions may be changed. It is equivalent to "keep" plus some additional processing, see https://github.com/GeoBosh/rbibutils/issues/7#issue-1020385889. - macros
-
additional bib files, usually containing bibtex macros, such as journal abbreviations.
- object
a
bibentryobject.- con
filename (a character string) or a text connection
- append
if
TRUEappend to the file.- text
a character vector.
- informat
the input format, defaults to
"bibtex".- key
-
a character vectors of key(s) to use for entries without cite keys. Should have the same number of elements as the number of such entries.
- ...
-
for
charTobib, arguments to be passed on toreadBiborbibConvert, see Details. Not used byreadBibandwriteBib(which throw error to avoid silently ignoring unknown arguments). - extra
if
TRUE, allow non-standard bibtex types.- fbibentry
a function to use for generating bib objects instead of
bibentry(), see Details.
Details
readBib is wrapper around bibConvert for import of
bibtex files into bibentry objects.
If direct = FALSE, the bibtex file is converted first to XML
intermediate, then the XML file is converted to bibentry. The
advantage of this is that it gives a standardised representation of
the bibtex input. Fields that cannot be mapped to the intermediate
format are generally omitted.
If direct = TRUE the input file is converted directly to
bibentry, without the XML intermediate step. This means that
non-standard fields in the bib entries are preserved in the bibentry
object.
Argument texChars, currently implemented only for the case
direct = TRUE, gives some control over the processing of TeX
sequences representing characters (such as accented Latin characters):
If it is "keep" (the default), such sequences are kept as in
the input. "convert" causes them to be converted to the
characters they represent. Finally, "export" exports characters
as TeX sequences, whenever possible.
The difference between "keep" and "export" is that
"keep" does not convert normal characters to TeX escapes, while
"export" does it if possible. For example, if the input file
contains the TeX sequence \"o
representing the letter o-umlaut, "keep" and "export"
will keep it as TeX sequence, while "convert" will convert it
to the character o-umlaut in the output encoding (normally UTF-8). On
the othe hand, if the input file contains the character o-umlaut, then
"keep" and "convert" will convert it to the output
encoding of o-umlaut, while "export" will export it as
\"o.
Currently, texChars = "export" does not process properly
mathematical formulas.
fbibentry, if supplied, should be a function with arguments
like bibentry to be used instead of utils::bibentry for
creating bib objects in R.
writeBib writes a bibentry object to a bibtex file.
charTobib is a convenience function for reading or converting
bibliography information, accepting the input from a
character vector rather than a file. If informat is missing it calls
readBib, otherwise bibConvert. In both cases
the remaining arguments are passed on and should be suitable for the
called function.
The files specified by argument macros are read in before those
in file. Currently this is implemented by concatenating the
files in the order they appear in c(macros, file). It is ok for
macros to be character(0).
Value
for readBib, a bibentry object. If extra is
TRUE it can also be bibentryExtra (which inherits from
bibentry). If fbibentry is a function the return value
is whatever it returns.
for writeBib, the bibentry object (invisibly)
See also
readBibentry and writeBibentry for
import/export to R code.
Examples
## create a bibentry object
bibs <- readBib(system.file("REFERENCES.bib", package = "rbibutils"),
encoding = "UTF-8")
## write bibs to a file
fn <- tempfile(fileext = ".bib")
writeBib(bibs, fn)
## see the contents of the file
readLines(fn) # or: file.show(fn)
#> [1] "@Manual{Rpackage:bibtex,"
#> [2] " author = {Romain Francois},"
#> [3] " title = {bibtex: bibtex parser},"
#> [4] " year = {2014},"
#> [5] " note = {R package version 0.4.0},"
#> [6] "}"
#> [7] ""
#> [8] "@Misc{Rpackage:Rdpack,"
#> [9] " author = {Georgi N Boshnakov},"
#> [10] " title = {{\\{}Rdpack{\\}}: Update and Manipulate Rd Documentation Objects},"
#> [11] " year = {2020},"
#> [12] " note = {R package version 2.0.0},"
#> [13] " doi = {10.5281/zenodo.3925612},"
#> [14] " url = {https://doi.org/10.5281/zenodo.3925612},"
#> [15] "}"
#> [16] ""
#> [17] "@Article{Rpackage:RefManageR,"
#> [18] " author = {Mathew William McLean},"
#> [19] " title = {RefManageR: Import and Manage BibTeX and BibLaTeX References in R},"
#> [20] " journal = {The Journal of Open Source Software},"
#> [21] " year = {2017},"
#> [22] " doi = {10.21105/joss.00338},"
#> [23] " url = {https://doi.org/10.21105/joss.00338},"
#> [24] "}"
#> [25] ""
#> [26] "@Misc{bibutils6.10,"
#> [27] " author = {Chris Putnam},"
#> [28] " title = {Library bibutils, version 6.10},"
#> [29] " year = {2020},"
#> [30] " url = {https://sourceforge.net/projects/bibutils/},"
#> [31] "}"
#> [32] ""
#> [33] "@Misc{Rpackage:easyPubMed,"
#> [34] " author = {Damiano Fantini},"
#> [35] " title = {easyPubMed: Search and Retrieve Scientific Publication Records from PubMed},"
#> [36] " year = {2019},"
#> [37] " note = {R package version 2.13},"
#> [38] " url = {https://CRAN.R-project.org/package=easyPubMed},"
#> [39] "}"
## import a bib file containing Chineese characters encoded with UTF-8:
ch_bib <- readBib(system.file("bib/xeCJK_utf8.bib", package = "rbibutils"))
ch_bib
#> 陈骁, 黄声华, 万山明, 庞珽 (2012).
#> “基于电无级变速器的内燃机最优控制策略及整车能量管理.” _电工技术学报_,
#> *27*(2), 133-138.
print(ch_bib, style = "R")
#> bibentry(bibtype = "Article",
#> key = "chen2012",
#> author = c(person(family = "陈骁"),
#> person(family = "黄声华"),
#> person(family = "万山明"),
#> person(family = "庞珽")),
#> title = "基于电无级变速器的内燃机最优控制策略及整车能量管理",
#> journal = "电工技术学报",
#> year = "2012",
#> volume = "27",
#> number = "2",
#> pages = "133--138")
## import a bib file encoded with the official Chineese encoding:
ch_bib2 <- readBib(system.file("bib/xeCJK_gb18030.bib", package = "rbibutils"),
encoding = "gb18030")
## a dummy reference with accented characters
## (in the file some are uft8, others are TeX escapes)
bibacc <- system.file("bib/latin1accents_utf8.bib", package = "rbibutils")
## export as UTF-8 characters
## this will print as true characters in suitable locale:
be <- readBib(bibacc, direct = TRUE, texChars = "convert")
print(be, style = "R")
#> bibentry(bibtype = "Article",
#> key = "test1",
#> author = person(given = "Kàrè",
#> family = "Lêáé"),
#> title = "Kàrè üä Lêáé",
#> journal = "Latin-1 accents",
#> year = "2020",
#> note = "Having the similar title and author is helpful for debugging since authors are processed differently from other fields. Here is a formula: $\\tan(\\alpha)$, $\\sin(\\delta)/\\delta \\to 1$, $\\sqrt{x}$.")
print(be, style = "bibtex")
#> @Article{test1,
#> author = {Kàrè Lêáé},
#> title = {Kàrè üä Lêáé},
#> journal = {Latin-1 accents},
#> year = {2020},
#> note = {Having the similar title and author is helpful for debugging since authors are processed differently from other fields. Here is a formula: $\tan(\alpha)$, $\sin(\delta)/\delta \to 1$, $\sqrt{x}$.},
#> }
## compare to the input file:
readLines(bibacc)
#> [1] " @ARTICLE{test1,"
#> [2] " AUTHOR = {Kàrè Lêáé},"
#> [3] " TITLE = {Kàrè \\\"u\\\"a Lêáé},"
#> [4] " JOURNAL = {Latin-1 accents},"
#> [5] " YEAR = {2020},"
#> [6] " NOTE = {Having the similar title and author is helpful for debugging since authors are"
#> [7] " processed differently from other fields. Here is a formula: $\\tan(\\alpha)$,"
#> [8] " $\\sin(\\delta)/\\delta \\to 1$, $\\sqrt{x}$.}"
#> [9] "}"
be1 <- readBib(bibacc, direct = TRUE)
be1a <- readBib(bibacc, direct = TRUE, texChars = "keep") # same
be1
#> Lêáé K (2020). “Kàrè üä Lêáé.” _Latin-1 accents_. Having the similar
#> title and author is helpful for debugging since authors are processed
#> differently from other fields. Here is a formula: $\tan(\alpha)$,
#> $\sin(\delta)/\delta\to1$, $\sqrt{x}$.
print(be1, style = "R")
#> bibentry(bibtype = "Article",
#> key = "test1",
#> author = person(given = "Kàrè",
#> family = "Lêáé"),
#> title = "Kàrè \\\"u\\\"a Lêáé",
#> journal = "Latin-1 accents",
#> year = "2020",
#> note = "Having the similar title and author is helpful for debugging since authors are processed differently from other fields. Here is a formula: $\\tan(\\alpha)$, $\\sin(\\delta)/\\delta \\to 1$, $\\sqrt{x}$.")
print(be1, style = "bibtex")
#> @Article{test1,
#> author = {Kàrè Lêáé},
#> title = {Kàrè \"u\"a Lêáé},
#> journal = {Latin-1 accents},
#> year = {2020},
#> note = {Having the similar title and author is helpful for debugging since authors are processed differently from other fields. Here is a formula: $\tan(\alpha)$, $\sin(\delta)/\delta \to 1$, $\sqrt{x}$.},
#> }
## export as TeX escapes, when possible
be2 <- readBib(bibacc, direct = TRUE, texChars = "export") ## same
be2
#> Lêáé K (2020). “Kàrè üä Lêáé.” _Latin-1 accents_. Having the similar
#> title and author is helpful for debugging since authors are processed
#> differently from other fields. Here is a formula: $\tan(\alpha)$,
#> $\sin(\delta)/\delta\to1$, $\sqrt{x}$.
print(be2, style = "R")
#> bibentry(bibtype = "Article",
#> key = "test1",
#> author = person(given = "K{\\`a}r{\\`e}",
#> family = "L{\\^e}{\\'a}{\\'e}"),
#> title = "K{\\`a}r{\\`e} \\\"u\\\"a L{\\^e}{\\'a}{\\'e}",
#> journal = "Latin-1 accents",
#> year = "2020",
#> note = "Having the similar title and author is helpful for debugging since authors are processed differently from other fields. Here is a formula: $\\tan(\\alpha)$, $\\sin(\\delta)/\\delta \\to 1$, $\\sqrt{x}$.")
print(be2, style = "bibtex")
#> @Article{test1,
#> author = {K{\`a}r{\`e} L{\^e}{\'a}{\'e}},
#> title = {K{\`a}r{\`e} \"u\"a L{\^e}{\'a}{\'e}},
#> journal = {Latin-1 accents},
#> year = {2020},
#> note = {Having the similar title and author is helpful for debugging since authors are processed differently from other fields. Here is a formula: $\tan(\alpha)$, $\sin(\delta)/\delta \to 1$, $\sqrt{x}$.},
#> }
## in older versions (up to 2.2.4) of rbibutils, "convert" converted
## a lot of TeX commands representing symbols to characters.
## This is no longer the case:
be3 <- readBib(bibacc, direct = TRUE, texChars = "convert")
## be3
print(be3, style = "R")
#> bibentry(bibtype = "Article",
#> key = "test1",
#> author = person(given = "Kàrè",
#> family = "Lêáé"),
#> title = "Kàrè üä Lêáé",
#> journal = "Latin-1 accents",
#> year = "2020",
#> note = "Having the similar title and author is helpful for debugging since authors are processed differently from other fields. Here is a formula: $\\tan(\\alpha)$, $\\sin(\\delta)/\\delta \\to 1$, $\\sqrt{x}$.")
## print(be3, style = "bibtex")
## charToBib
##
## get a bibtex reference for R
Rcore <- format(citation(), style = "bibtex")
## add a citation key
Rcore <- sub("@Manual{", "@Manual{Rcore", Rcore, fixed = TRUE)
cat(Rcore, sep = "\n")
#> @Manual{Rcore,
#> title = {R: A Language and Environment for Statistical Computing},
#> author = {{R Core Team}},
#> organization = {R Foundation for Statistical Computing},
#> address = {Vienna, Austria},
#> year = {2023},
#> url = {https://www.R-project.org/},
#> }
beRcore <- charToBib(Rcore)
beRcore
#> R Core Team (2023). _R: A Language and Environment for Statistical
#> Computing_. <https://www.R-project.org/>.
class(beRcore)
#> [1] "bibentry"
print(beRcore, style = "R")
#> bibentry(bibtype = "Manual",
#> key = "Rcore",
#> author = person(family = "R Core Team"),
#> title = "R: A Language and Environment for Statistical Computing",
#> year = "2023",
#> publisher = "R Foundation for Statistical Computing",
#> address = "Vienna, Austria",
#> url = "https://www.R-project.org/")
## bibtex entries generated by citation() don't have cite keys.
## this sets the key to 'Rcore'
beRcore <- charToBib(toBibtex(citation()), key = "Rcore")
beRcore$key == "Rcore" # TRUE
#> [1] TRUE
## this sets two keys
bemore <- charToBib(toBibtex( c(citation(), citation("rbibutils"))),
key = c("Rcore", "Rpackage:rbibutils"))
all.equal(names(bemore), c("Rcore", "Rpackage:rbibutils"))
#> [1] TRUE
## a large example with several files - needs internet access;
## it is better to clone repository https://github.com/iridia-ulb/references
## and work on local files
##
## iridia_mac <- c("abbrev.bib", "authors.bib", "journals.bib", "crossref.bib")
## iridia_biblio <- "biblio.bib"
##
## iridia_raw_url <- "https://raw.githubusercontent.com/iridia-ulb/references/master"
## iridia_mac_url <- file.path(iridia_raw_url, iridia_mac)
## iridia_biblio_url <- file.path(iridia_raw_url, iridia_biblio)
##
## bibdir <- tempdir()
## iridia_mac_loc <- file.path(bibdir, iridia_mac)
## iridia_biblio_loc <- file.path(bibdir, iridia_biblio)
##
## ## download the files to bibdir
## sapply(c(iridia_biblio_url, iridia_mac_url),
## function(x) download.file(x, file.path(bibdir, basename(x))))
##
## iridia <- readBib(iridia_biblio_loc, direct = TRUE, macros = iridia_mac_loc)
## iridia[1]
## print(iridia[1], style = "R")
## toBibtex(iridia[1]) # or: print(iridia[1], style = "bibtex")
## length(iridia) # 2576 at the time of writing
unlink(fn)