title	author	date	bibliography
An introduction to knitcitations	Carl Boettiger	27 May 2014	references.bib

knitcitations

knitcitations is an R package designed to add dynamic citations to dynamic documents created with Yihui's knitr package.

Installation

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").

Quick start: rmarkdown (pandoc) mode

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 by DOI

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.

Cite by URL

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].

Cite bibtex and bibentry objects directly

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).

Re-using Keys

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.

Displaying the final bibliography

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.

cboettig/knitcitations