Bibliographies

Specifying a Bibliography

Pandoc can automatically generate citations and a bibliography in a number of styles. In order to use this feature, you will need to specify a bibliography file using the bibliography metadata field in a YAML metadata section. For example:

---
title: "Sample Document"
output: html_document
bibliography: bibliography.bib
---

The bibliography may have any of these formats:

Format File extension
MODS .mods
BibLaTeX .bib
BibTeX .bibtex
RIS .ris
EndNote .enl
EndNote XML .xml
ISI .wos
MEDLINE .medline
Copac .copac
JSON citeproc .json

Note that .bib can generally be used with both BibTeX and BibLaTeX files, but you can use .bibtex to force BibTeX.

Inline References

Alternatively you can use a references field in the document’s YAML metadata. This should include an array of YAML-encoded references, for example:

---
references:
- id: fenner2012a
  title: One-click science marketing
  author:
  - family: Fenner
    given: Martin
  container-title: Nature Materials
  volume: 11
  URL: 'http://dx.doi.org/10.1038/nmat3283'
  DOI: 10.1038/nmat3283
  issue: 4
  publisher: Nature Publishing Group
  page: 261-263
  type: article-journal
  issued:
    year: 2012
    month: 3
---

Bibliography Placement

Bibliographies will be placed at the end of the document. Normally, you will want to end your document with an appropriate header:

last paragraph...

# References

The bibliography will be inserted after this header.

Citations

Citation Syntax

Citations go inside square brackets and are separated by semicolons. Each citation must have a key, composed of ‘@’ + the citation identifier from the database, and may optionally have a prefix, a locator, and a suffix. Here are some examples:

Blah blah [see @doe99, pp. 33-35; also @smith04, ch. 1].

Blah blah [@doe99, pp. 33-35, 38-39 and *passim*].

Blah blah [@smith04; @doe99].

A minus sign (-) before the @ will suppress mention of the author in the citation. This can be useful when the author is already mentioned in the text:

Smith says blah [-@smith04].

You can also write an in-text citation, as follows:

@smith04 says blah.

@smith04 [p. 33] says blah.

Unused References (nocite)

If you want to include items in the bibliography without actually citing them in the body text, you can define a dummy nocite metadata field and put the citations there:

---
nocite: | 
  @item1, @item2
...

@item3

In this example, the document will contain a citation for item3 only, but the bibliography will contain entries for item1, item2, and item3.

Citation Styles

By default, pandoc will use a Chicago author-date format for citations and references. To use another style, you will need to specify a CSL 1.0 style file in the csl metadata field. For example:

---
title: "Sample Document"
output: html_document
bibliography: bibliography.bib
csl: biomed-central.csl
---

A primer on creating and modifying CSL styles can be found at http://citationstyles.org/downloads/primer.html. A repository of CSL styles can be found at https://github.com/citation-style-language/styles. See also http://zotero.org/styles for easy browsing.

Citations for PDF Output

By default, citations are generated by the utility pandoc-citeproc, and it works for all output formats. When the output is LaTeX/PDF, you can also use LaTeX packages (e.g. natbib) to generate citations; see [PDF documents] for details.

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