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27 May 2014
knitcitations is an R package designed to add dynamic
citations to dynamic documents created with Yihui’s knitr package.
Install the development version directly from Github
library(devtools)
install_github("cboettig/knitcitations")Or install the current release from your CRAN mirror with
install.packages("knitcitations").
Start by loading the library. It is usually good to also clear the bibliographic environment after loading the library, in case any citations are already stored there:
library("knitcitations")
cleanbib()Set pandoc as the default format:
options("citation_format" = "pandoc")(Note: The old method will eventually be deprecated. For documents
using knitcitations <= 0.5 it will become necessary to
set this as "compatibility").
Cite an article by DOI and the full citation information is gathered
automatically. By default this now generates a citation in
pandoc-flavored-markdown format. We use the inline command
citep("10.1890/11-0011.1") to create this citation [@Abrams_2012].
An in-text citation is generated with citet, such as
citet("10.1098/rspb.2013.1372") creating the citation to
@Boettiger_2013.
Not all the literature we may wish to cite includes DOIs, such as arXiv preprints, Wikipedia pages, or other
academic blogs. Even when a DOI is present it is not always trivial to
locate. With version 0.4-0, knitcitations can produce
citations given any URL using the Greycite API. For instance,
we can use the call
citep("http://knowledgeblog.org/greycite") to generate the
citation to the Greycite tool [@greycite2739].
We can also use bibentry objects such as R provides for
citing packages (using R’s citation() function):
citep(citation("knitr") produces [@Xie_2014; @Xie_2013;
@Xie_2014a]. Note that this package includes citations to three
objects, and pandoc correctly avoids duplicating the author names. In
pandoc mode, we can still use traditional pandoc-markdown citations like
@Boettiger2013 which will render as @Boettiger2013 without any R code,
provided the citation is already in the .bib file we name
(see below).
When the citation is called, a key in the format
FirstAuthorsLastName_Year is automatically created for this
citation, so we can now continue to cite this article without
remembering the DOI, using the command citep("Abrams_2012")
creates the citation [@Abrams_2012] without mistaking it for
a new article.
At the end of the document, include a chunk containing the command:
write.bibtex(file="references.bib")Use the chunk options echo=FALSE and
message=FALSE to hide the chunk command and output.
This creates a Bibtex file with the name given. Pandoc can then be used to compile the markdown into HTML, MS Word, LaTeX, PDF, or many other formats, each with the desired journal styling. Pandoc is now integrated with RStudio through the rmarkdown package. Pandoc appends these references to the end of the markdown document automatically. In this example, we have added a yaml header to our Rmd file which indicates the name of the bib file being used, and the optional link to a CSL stylesheet which formats the output for the ESA journals:
---
bibliography: "references.bib"
csl: "ecology.csl"
output:
html_document
---Then calling rmarkdown::render("intro.Rmd") from R on
the tutorial compiles the output markdown, with references in the format
of the ESA journals.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.