Pandoc Yaml Bibliography Sample

I am trying to use a custom citation style in a markdown file, but the citation uses the default (Chicago) style each time I knit. I have tried changing the output format from a JS reveal presentation to an HTML document to a PDF document, but it still does not work. I am using the knitcitations package to cite using the document's DOI, and the bibliography() function to write the bibliography. I have also tried using the apa.csl style found on Zotero, yet the citation is still done in the default styple. The apa.csl file is stored in the same folder as the file that I am trying to use citations in, as is the newbiblio.bib file, in which I have stored the bibliographical information for the item I want to cite.

Below is my markdown code:

This link (http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html) says that I should be able to format my YAML header like this:

However, when I do that, the file knits to a markdown (.md) file, but it is not processed into the output. I recieve this error:

The contents of my .bib file are:

I also do not understand why the biblio-style option in the YAML header does not to do anything. Essentially, all I need is a way to use a custom citation style I have already made with a markdown document. Any help would be greatly appreciated!

yamlknitrr-markdownpandoccitations

Pandoc User’s Guide

Synopsis

[options] [input-file]…

Description

Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library.

Pandoc can read Markdown, CommonMark, PHP Markdown Extra, GitHub-Flavored Markdown, MultiMarkdown, and (subsets of) Textile, reStructuredText, HTML, LaTeX, MediaWiki markup, TWiki markup, TikiWiki markup, Creole 1.0, Haddock markup, OPML, Emacs Org mode, DocBook, JATS, Muse, txt2tags, Vimwiki, EPUB, ODT, and Word docx.

Pandoc can write plain text, Markdown, CommonMark, PHP Markdown Extra, GitHub-Flavored Markdown, MultiMarkdown, reStructuredText, XHTML, HTML5, LaTeX (including slide shows), ConTeXt, RTF, OPML, DocBook, JATS, OpenDocument, ODT, Word docx, GNU Texinfo, MediaWiki markup, DokuWiki markup, ZimWiki markup, Haddock markup, EPUB (v2 or v3), FictionBook2, Textile, groff man, groff ms, Emacs Org mode, AsciiDoc, InDesign ICML, TEI Simple, Muse, PowerPoint slide shows and Slidy, Slideous, DZSlides, reveal.js or S5 HTML slide shows. It can also produce PDF output on systems where LaTeX, ConTeXt, , , , or is installed.

Pandoc’s enhanced version of Markdown includes syntax for tables, definition lists, metadata blocks, blocks, footnotes and citations, embedded LaTeX (including math), Markdown inside HTML block elements, and much more. These enhancements, described further under Pandoc’s Markdown, can be disabled using the format.

Pandoc has a modular design: it consists of a set of readers, which parse text in a given format and produce a native representation of the document (like an abstract syntax tree or AST), and a set of writers, which convert this native representation into a target format. Thus, adding an input or output format requires only adding a reader or writer. Users can also run custom pandoc filters to modify the intermediate AST.

Because pandoc’s intermediate representation of a document is less expressive than many of the formats it converts between, one should not expect perfect conversions between every format and every other. Pandoc attempts to preserve the structural elements of a document, but not formatting details such as margin size. And some document elements, such as complex tables, may not fit into pandoc’s simple document model. While conversions from pandoc’s Markdown to all formats aspire to be perfect, conversions from formats more expressive than pandoc’s Markdown can be expected to be lossy.

Using

If no input-files are specified, input is read from stdin. Output goes to stdout by default. For output to a file, use the option:

By default, pandoc produces a document fragment. To produce a standalone document (e.g. a valid HTML file including and ), use the or flag:

For more information on how standalone documents are produced, see Templates below.

If multiple input files are given, will concatenate them all (with blank lines between them) before parsing. (Use to parse files individually.)

Specifying formats

The format of the input and output can be specified explicitly using command-line options. The input format can be specified using the option, the output format using the option. Thus, to convert from Markdown to LaTeX, you could type:

To convert from HTML to Markdown:

Supported input and output formats are listed below under Options (see for input formats and for output formats). You can also use and to print lists of supported formats.

If the input or output format is not specified explicitly, will attempt to guess it from the extensions of the filenames. Thus, for example,

will convert from Markdown to LaTeX. If no output file is specified (so that output goes to stdout), or if the output file’s extension is unknown, the output format will default to HTML. If no input file is specified (so that input comes from stdin), or if the input files’ extensions are unknown, the input format will be assumed to be Markdown.

Character encoding

Pandoc uses the UTF-8 character encoding for both input and output. If your local character encoding is not UTF-8, you should pipe input and output through :

Note that in some output formats (such as HTML, LaTeX, ConTeXt, RTF, OPML, DocBook, and Texinfo), information about the character encoding is included in the document header, which will only be included if you use the option.

Creating a PDF

To produce a PDF, specify an output file with a extension:

By default, pandoc will use LaTeX to create the PDF, which requires that a LaTeX engine be installed (see below).

Alternatively, pandoc can use ConTeXt, , or any of the following HTML/CSS-to-PDF-engines, to create a PDF: , or . To do this, specify an output file with a extension, as before, but add the option or , , or to the command line ( defaults to ).

PDF output can be controlled using variables for LaTeX (if LaTeX is used) and variables for ConTeXt (if ConTeXt is used). When using an HTML/CSS-to-PDF-engine, affects the output. If is used, then the variables , , , , , and will affect the output.

To debug the PDF creation, it can be useful to look at the intermediate representation: instead of , use for example to output the generated LaTeX. You can then test it with .

When using LaTeX, the following packages need to be available (they are included with all recent versions of TeX Live): , , , , , , (if the option is used), , , , and (if the document contains images), , (with ), , (with the variable set), (with ), and (with ). The use of or as the LaTeX engine requires . uses (with ), , and (with the variable set). If the variable is set, will use instead of . The and packages are used if available, and will be used for typography if added to the template or included in any header file. The , , , and packages can optionally be used for citation rendering.

Reading from the Web

Instead of an input file, an absolute URI may be given. In this case pandoc will fetch the content using HTTP:

It is possible to supply a custom User-Agent string or other header when requesting a document from a URL:

Options

General options

FORMAT, FORMAT, FORMAT, FORMAT

Specify input format. FORMAT can be (native Haskell), (JSON version of native AST), (pandoc’s extended Markdown), (original unextended Markdown), (PHP Markdown Extra), (MultiMarkdown), (GitHub-Flavored Markdown), (CommonMark Markdown), (Textile), (reStructuredText), (HTML), (DocBook), (txt2tags), (docx), (ODT), (EPUB), (OPML), (Emacs Org mode), (MediaWiki markup), (TWiki markup), (TikiWiki markup), (Creole 1.0), (Haddock markup), or (LaTeX). ( provides deprecated and less accurate support for Github-Flavored Markdown; please use instead, unless you need to use extensions other than .) Extensions can be individually enabled or disabled by appending or to the format name. See Extensions below, for a list of extensions and their names. See and , below.

FORMAT, FORMAT, FORMAT, FORMAT

Specify output format. FORMAT can be (native Haskell), (JSON version of native AST), (plain text), (pandoc’s extended Markdown), (original unextended Markdown), (PHP Markdown Extra), (MultiMarkdown), (GitHub-Flavored Markdown), (CommonMark Markdown), (reStructuredText), (XHTML 1.0 Transitional), or (HTML5/XHTML polyglot markup), (LaTeX), (LaTeX beamer slide show), (ConTeXt), (groff man), (MediaWiki markup), (DokuWiki markup), (ZimWiki markup), (Textile), (Emacs Org mode), (GNU Texinfo), (OPML), or (DocBook 4), (DocBook 5), (JATS XML), (OpenDocument), (OpenOffice text document), (Word docx), (Haddock markup), (rich text format), (EPUB v2 book), or (EPUB v3), (FictionBook2 e-book), (AsciiDoc), (InDesign ICML), (TEI Simple), (Slidy HTML and JavaScript slide show), (Slideous HTML and JavaScript slide show), (DZSlides HTML5 + JavaScript slide show), (reveal.js HTML5 + JavaScript slide show), (S5 HTML and JavaScript slide show), (PowerPoint slide show) or the path of a custom lua writer (see Custom writers, below). ( provides deprecated and less accurate support for Github-Flavored Markdown; please use instead, unless you use extensions that do not work with .) Note that , , and output will not be directed to stdout unless forced with . Extensions can be individually enabled or disabled by appending or to the format name. See Extensions below, for a list of extensions and their names. See and , below.

FILE, FILE

Write output to FILE instead of stdout. If FILE is , output will go to stdout, even if a non-textual format (, , , ) is specified.

DIRECTORY

Specify the user data directory to search for pandoc data files. If this option is not specified, the default user data directory will be used. This is, in UNIX:

in Windows XP:

and in Windows Vista or later:

You can find the default user data directory on your system by looking at the output of . A , , , , , , or directory placed in this directory will override pandoc’s normal defaults.

Generate a bash completion script. To enable bash completion with pandoc, add this to your :

Give verbose debugging output. Currently this only has an effect with PDF output.

Suppress warning messages.

Exit with error status if there are any warnings.

FILE

Write log messages in machine-readable JSON format to FILE. All messages above DEBUG level will be written, regardless of verbosity settings (, ).

List supported input formats, one per line.

List supported output formats, one per line.

[FORMAT]

List supported extensions, one per line, preceded by a or indicating whether it is enabled by default in FORMAT. If FORMAT is not specified, defaults for pandoc’s Markdown are given.

List supported languages for syntax highlighting, one per line.

List supported styles for syntax highlighting, one per line. See .

,

Print version.

,

Show usage message.

Reader options

NUMBER

Specify the base level for headers (defaults to 1).

Deprecated. Use the extension instead. Ignore paragraphs with no content. This option is useful for converting word processing documents where users have used empty paragraphs to create inter-paragraph space.

CLASSES

Specify classes to use for indented code blocks–for example, or . Multiple classes may be separated by spaces or commas.

EXTENSION

Specify a default extension to use when image paths/URLs have no extension. This allows you to use the same source for formats that require different kinds of images. Currently this option only affects the Markdown and LaTeX readers.

Parse each file individually before combining for multifile documents. This will allow footnotes in different files with the same identifiers to work as expected. If this option is set, footnotes and links will not work across files. Reading binary files (docx, odt, epub) implies .

PROGRAM

Specify an executable to be used as a filter transforming the pandoc AST after the input is parsed and before the output is written. The executable should read JSON from stdin and write JSON to stdout. The JSON must be formatted like pandoc’s own JSON input and output. The name of the output format will be passed to the filter as the first argument. Hence,

is equivalent to

The latter form may be useful for debugging filters.

Filters may be written in any language. exports to facilitate writing filters in Haskell. Those who would prefer to write filters in python can use the module , installable from PyPI. There are also pandoc filter libraries in PHP, perl, and JavaScript/node.js.

In order of preference, pandoc will look for filters in

  1. a specified full or relative path (executable or non-executable)

  2. (executable or non-executable) where is the user data directory (see , above).

  3. (executable only)

Filters and lua-filters are applied in the order specified on the command line.

SCRIPT

Transform the document in a similar fashion as JSON filters (see ), but use pandoc’s build-in lua filtering system. The given lua script is expected to return a list of lua filters which will be applied in order. Each lua filter must contain element-transforming functions indexed by the name of the AST element on which the filter function should be applied.

The lua module provides helper functions for element creation. It is always loaded into the script’s lua environment.

The following is an example lua script for macro-expansion:

KEY[VAL], KEY[VAL]

Set the metadata field KEY to the value VAL. A value specified on the command line overrides a value specified in the document. Values will be parsed as YAML boolean or string values. If no value is specified, the value will be treated as Boolean true. Like , causes template variables to be set. But unlike , affects the metadata of the underlying document (which is accessible from filters and may be printed in some output formats).

,

Preserve tabs instead of converting them to spaces (the default). Note that this will only affect tabs in literal code spans and code blocks; tabs in regular text will be treated as spaces.

NUMBER

Specify the number of spaces per tab (default is 4).

||

Specifies what to do with insertions, deletions, and comments produced by the MS Word “Track Changes” feature. (the default), inserts all insertions, and ignores all deletions. inserts all deletions and ignores insertions. Both and ignore comments. puts in insertions, deletions, and comments, wrapped in spans with , , , and classes, respectively. The author and time of change is included. is useful for scripting: only accepting changes from a certain reviewer, say, or before a certain date. If a paragraph is inserted or deleted, produces a span with the class / before the affected paragraph break. This option only affects the docx reader.

DIR

Extract images and other media contained in or linked from the source document to the path DIR, creating it if necessary, and adjust the images references in the document so they point to the extracted files. If the source format is a binary container (docx, epub, or odt), the media is extracted from the container and the original filenames are used. Otherwise the media is read from the file system or downloaded, and new filenames are constructed based on SHA1 hashes of the contents.

FILE

Specifies a custom abbreviations file, with abbreviations one to a line. If this option is not specified, pandoc will read the data file from the user data directory or fall back on a system default. To see the system default, use . The only use pandoc makes of this list is in the Markdown reader. Strings ending in a period that are found in this list will be followed by a nonbreaking space, so that the period will not produce sentence-ending space in formats like LaTeX.

General writer options

,

Produce output with an appropriate header and footer (e.g. a standalone HTML, LaTeX, TEI, or RTF file, not a fragment). This option is set automatically for , , , , , and output.

FILE

Use FILE as a custom template for the generated document. Implies . See Templates, below, for a description of template syntax. If no extension is specified, an extension corresponding to the writer will be added, so that looks for for HTML output. If the template is not found, pandoc will search for it in the subdirectory of the user data directory (see ). If this option is not used, a default template appropriate for the output format will be used (see ).

KEY[VAL], KEY[VAL]

Set the template variable KEY to the value VAL when rendering the document in standalone mode. This is generally only useful when the option is used to specify a custom template, since pandoc automatically sets the variables used in the default templates. If no VAL is specified, the key will be given the value .

FORMAT, FORMAT

Print the system default template for an output FORMAT. (See for a list of possible FORMATs.) Templates in the user data directory are ignored.

FILE

Print a system default data file. Files in the user data directory are ignored.

||

Manually specify line endings: (Windows), (macOS/Linux/UNIX), or (line endings appropriate to the OS on which pandoc is being run). The default is .

=NUMBER

Specify the dpi (dots per inch) value for conversion from pixels to inch/centimeters and vice versa. The default is 96dpi. Technically, the correct term would be ppi (pixels per inch).

||

Determine how text is wrapped in the output (the source code, not the rendered version). With (the default), pandoc will attempt to wrap lines to the column width specified by (default 72). With , pandoc will not wrap lines at all. With , pandoc will attempt to preserve the wrapping from the source document (that is, where there are nonsemantic newlines in the source, there will be nonsemantic newlines in the output as well). Automatic wrapping does not currently work in HTML output.

NUMBER

Specify length of lines in characters. This affects text wrapping in the generated source code (see ). It also affects calculation of column widths for plain text tables (see Tables below).

,

Include an automatically generated table of contents (or, in the case of , , , , , , or , an instruction to create one) in the output document. This option has no effect on , , , or output.

NUMBER

Specify the number of section levels to include in the table of contents. The default is 3 (which means that level 1, 2, and 3 headers will be listed in the contents).

Strip out HTML comments in the Markdown or Textile source, rather than passing them on to Markdown, Textile or HTML output as raw HTML. This does not apply to HTML comments inside raw HTML blocks when the extension is not set.

Disables syntax highlighting for code blocks and inlines, even when a language attribute is given.

STYLE|FILE

Specifies the coloring style to be used in highlighted source code. Options are (the default), , , , , , , and . For more information on syntax highlighting in pandoc, see Syntax highlighting, below. See also .

Instead of a STYLE name, a JSON file with extension may be supplied. This will be parsed as a KDE syntax highlighting theme and (if valid) used as the highlighting style.

To generate the JSON version of an existing style, use .

STYLE|FILE

Prints a JSON version of a highlighting style, which can be modified, saved with a extension, and used with .

FILE

Instructs pandoc to load a KDE XML syntax definition file, which will be used for syntax highlighting of appropriately marked code blocks. This can be used to add support for new languages or to use altered syntax definitions for existing languages.

FILE, FILE

Include contents of FILE, verbatim, at the end of the header. This can be used, for example, to include special CSS or JavaScript in HTML documents. This option can be used repeatedly to include multiple files in the header. They will be included in the order specified. Implies .

FILE, FILE

Include contents of FILE, verbatim, at the beginning of the document body (e.g. after the tag in HTML, or the command in LaTeX). This can be used to include navigation bars or banners in HTML documents. This option can be used repeatedly to include multiple files. They will be included in the order specified. Implies .

FILE, FILE

Include contents of FILE, verbatim, at the end of the document body (before the tag in HTML, or the command in LaTeX). This option can be used repeatedly to include multiple files. They will be included in the order specified. Implies .

SEARCHPATH

List of paths to search for images and other resources. The paths should be separated by on Linux, UNIX, and macOS systems, and by on Windows. If is not specified, the default resource path is the working directory. Note that, if is specified, the working directory must be explicitly listed or it will not be searched. For example: will search the working directory and the subdirectory, in that order.

NAMEVAL

Set the request header NAME to the value VAL when making HTTP requests (for example, when a URL is given on the command line, or when resources used in a document must be downloaded).

Options affecting specific writers

Produce a standalone HTML file with no external dependencies, using URIs to incorporate the contents of linked scripts, stylesheets, images, and videos. Implies . The resulting file should be “self-contained,” in the sense that it needs no external files and no net access to be displayed properly by a browser. This option works only with HTML output formats, including , , , , , , , , and . Scripts, images, and stylesheets at absolute URLs will be downloaded; those at relative URLs will be sought relative to the working directory (if the first source file is local) or relative to the base URL (if the first source file is remote). Elements with the attribute will be left alone; the documents they link to will not be incorporated in the document. Limitation: resources that are loaded dynamically through JavaScript cannot be incorporated; as a result, does not work with , and some advanced features (e.g. zoom or speaker notes) may not work in an offline “self-contained” slide show.

Use tags for quotes in HTML.

Use only ASCII characters in output. Currently supported only for HTML and DocBook output (which uses numerical entities instead of UTF-8 when this option is selected).

Use reference-style links, rather than inline links, in writing Markdown or reStructuredText. By default inline links are used. The placement of link references is affected by the option.

||

Specify whether footnotes (and references, if is set) are placed at the end of the current (top-level) block, the current section, or the document. The default is . Currently only affects the markdown writer.

Use ATX-style headers in Markdown and AsciiDoc output. The default is to use setext-style headers for levels 1-2, and then ATX headers. (Note: for output, ATX headers are always used.)

Treat top-level headers as the given division type in LaTeX, ConTeXt, DocBook, and TEI output. The hierarchy order is part, chapter, then section; all headers are shifted such that the top-level header becomes the specified type. The default behavior is to determine the best division type via heuristics: unless other conditions apply, is chosen. When the LaTeX document class is set to , , or (unless the option is specified), is implied as the setting for this option. If is the output format, specifying either or will cause top-level headers to become , while second-level headers remain as their default type.

,

Number section headings in LaTeX, ConTeXt, HTML, or EPUB output. By default, sections are not numbered. Sections with class will never be numbered, even if is specified.

NUMBER[NUMBER]

Offset for section headings in HTML output (ignored in other output formats). The first number is added to the section number for top-level headers, the second for second-level headers, and so on. So, for example, if you want the first top-level header in your document to be numbered “6”, specify . If your document starts with a level-2 header which you want to be numbered “1.5”, specify . Offsets are 0 by default. Implies .

Use the package for LaTeX code blocks

,

Make list items in slide shows display incrementally (one by one). The default is for lists to be displayed all at once.

NUMBER

Specifies that headers with the specified level create slides (for , , , , ). Headers above this level in the hierarchy are used to divide the slide show into sections; headers below this level create subheads within a slide. Note that content that is not contained under slide-level headers will not appear in the slide show. The default is to set the slide level based on the contents of the document; see Structuring the slide show.

Wrap sections in tags (or tags for ), and attach identifiers to the enclosing (or ) rather than the header itself. See Header identifiers, below.

||

Specify a method for obfuscating links in HTML documents. leaves links as they are. obfuscates them using JavaScript. obfuscates them by printing their letters as decimal or hexadecimal character references. The default is .

STRING

Specify a prefix to be added to all identifiers and internal links in HTML and DocBook output, and to footnote numbers in Markdown and Haddock output. This is useful for preventing duplicate identifiers when generating fragments to be included in other pages.

STRING, STRING

Specify STRING as a prefix at the beginning of the title that appears in the HTML header (but not in the title as it appears at the beginning of the HTML body). Implies .

URL, URL

Link to a CSS style sheet. This option can be used repeatedly to include multiple files. They will be included in the order specified.

A stylesheet is required for generating EPUB. If none is provided using this option (or the metadata field), pandoc will look for a file in the user data directory (see ). If it is not found there, sensible defaults will be used.

FILE

Use the specified file as a style reference in producing a docx or ODT file.

Docx

For best results, the reference docx should be a modified version of a docx file produced using pandoc. The contents of the reference docx are ignored, but its stylesheets and document properties (including margins, page size, header, and footer) are used in the new docx. If no reference docx is specified on the command line, pandoc will look for a file in the user data directory (see ). If this is not found either, sensible defaults will be used.

To produce a custom , first get a copy of the default : . Then open in Word, modify the styles as you wish, and save the file. For best results, do not make changes to this file other than modifying the styles used by pandoc: [paragraph] Normal, Body Text, First Paragraph, Compact, Title, Subtitle, Author, Date, Abstract, Bibliography, Heading 1, Heading 2, Heading 3, Heading 4, Heading 5, Heading 6, Heading 7, Heading 8, Heading 9, Block Text, Footnote Text, Definition Term, Definition, Caption, Table Caption, Image Caption, Figure, Captioned Figure, TOC Heading; [character] Default Paragraph Font, Body Text Char, Verbatim Char, Footnote Reference, Hyperlink; [table] Table.

ODT

For best results, the reference ODT should be a modified version of an ODT produced using pandoc. The contents of the reference ODT are ignored, but its stylesheets are used in the new ODT. If no reference ODT is specified on the command line, pandoc will look for a file in the user data directory (see ). If this is not found either, sensible defaults will be used.

To produce a custom , first get a copy of the default : . Then open in LibreOffice, modify the styles as you wish, and save the file.

PowerPoint

Any template included with a recent install of Microsoft PowerPoint (either with or extension) should work, as will most templates derived from these.

The specific requirement is that the template should contain the following four layouts as its first four layouts:

  1. Title Slide
  2. Title and Content
  3. Section Header
  4. Two Content

All templates included with a recent version of MS PowerPoint will fit these criteria. (You can click on under the menu to check.)

You can also modify the default : first run , and then modify in MS PowerPoint (pandoc will use the first four layout slides, as mentioned above).

FILE

Use the specified image as the EPUB cover. It is recommended that the image be less than 1000px in width and height. Note that in a Markdown source document you can also specify in a YAML metadata block (see EPUB Metadata, below).

FILE

Look in the specified XML file for metadata for the EPUB. The file should contain a series of Dublin Core elements. For example:

By default, pandoc will include the following metadata elements: (from the document title), (from the document authors), (from the document date, which should be in ISO 8601 format), (from the variable, or, if is not set, the locale), and (a randomly generated UUID). Any of these may be overridden by elements in the metadata file.

Note: if the source document is Markdown, a YAML metadata block in the document can be used instead. See below under EPUB Metadata.

FILE

Embed the specified font in the EPUB. This option can be repeated to embed multiple fonts. Wildcards can also be used: for example, . However, if you use wildcards on the command line, be sure to escape them or put the whole filename in single quotes, to prevent them from being interpreted by the shell. To use the embedded fonts, you will need to add declarations like the following to your CSS (see ):

NUMBER

Specify the header level at which to split the EPUB into separate “chapter” files. The default is to split into chapters at level 1 headers. This option only affects the internal composition of the EPUB, not the way chapters and sections are displayed to users. Some readers may be slow if the chapter files are too large, so for large documents with few level 1 headers, one might want to use a chapter level of 2 or 3.

DIRNAME

Specify the subdirectory in the OCF container that is to hold the EPUB-specific contents. The default is . To put the EPUB contents in the top level, use an empty string.

|||||||

Use the specified engine when producing PDF output. The default is . If the engine is not in your PATH, the full path of the engine may be specified here.

STRING

Use the given string as a command-line argument to the . If used multiple times, the arguments are provided with spaces between them. Note that no check for duplicate options is done.

Citation rendering

FILE

Set the field in the document’s metadata to FILE, overriding any value set in the metadata, and process citations using . (This is equivalent to .) If or is also supplied, is not used, making this equivalent to . If you supply this argument multiple times, each FILE will be added to bibliography.

FILE

Set the field in the document’s metadata to FILE, overriding any value set in the metadata. (This is equivalent to .) This option is only relevant with .

FILE

Set the field in the document’s metadata to FILE, overriding any value set in the metadata. (This is equivalent to .) This option is only relevant with .

Use for citations in LaTeX output. This option is not for use with the filter or with PDF output. It is intended for use in producing a LaTeX file that can be processed with .

Use for citations in LaTeX output. This option is not for use with the filter or with PDF output. It is intended for use in producing a LaTeX file that can be processed with or .

Math rendering in HTML

The default is to render TeX math as far as possible using Unicode characters. Formulas are put inside a with , so that they may be styled differently from the surrounding text if needed. However, this gives acceptable results only for basic math, usually you will want to use or another of the following options.

[URL]

Use MathJax to display embedded TeX math in HTML output. TeX math will be put between (for inline math) or (for display math) and wrapped in tags with class . Then the MathJax JavaScript will render it. The URL should point to the load script. If a URL is not provided, a link to the Cloudflare CDN will be inserted.

Convert TeX math to MathML (in , , , , and ). This is the default in output. Note that currently only Firefox and Safari (and select e-book readers) natively support MathML.

[URL]

Convert TeX formulas to tags that link to an external script that converts formulas to images. The formula will be URL-encoded and concatenated with the URL provided. For SVG images you can for example use . If no URL is specified, the CodeCogs URL generating PNGs will be used (). Note: the option will affect Markdown output as well as HTML, which is useful if you’re targeting a version of Markdown without native math support.

[URL]

Use KaTeX to display embedded TeX math in HTML output. The URL is the base URL for the KaTeX library. If a URL is not provided, a link to the KaTeX CDN will be inserted.

URL

The URL should point to the stylesheet. If this option is not specified, a link to the KaTeX CDN will be inserted. Note that this option does not imply .

[URL], [URL]

Deprecated. Use the LaTeXMathML script to display embedded TeX math in HTML output. TeX math will be displayed between or characters and put in tags with class . The LaTeXMathML JavaScript will then change it to MathML. Note that currently only Firefox and Safari (and select e-book readers) natively support MathML. To insert a link the script, provide a URL.

[URL]

Deprecated. Use jsMath (the predecessor of MathJax) to display embedded TeX math in HTML output. TeX math will be put inside tags (for inline math) or tags (for display math) with class and rendered by the jsMath script. The URL should point to the script (e.g. ); if provided, it will be linked to in the header of standalone HTML documents. If a URL is not provided, no link to the jsMath load script will be inserted; it is then up to the author to provide such a link in the HTML template.

Deprecated. Enclose TeX math in tags in HTML output. The resulting HTML can then be processed by gladTeX to produce images of the typeset formulas and an HTML file with links to these images. So, the procedure is:

[URL]

Deprecated. Render TeX math using the mimeTeX CGI script, which generates an image for each TeX formula. This should work in all browsers. If URL is not specified, it is assumed that the script is at .

Options for wrapper scripts

Print information about command-line arguments to stdout, then exit. This option is intended primarily for use in wrapper scripts. The first line of output contains the name of the output file specified with the option, or (for stdout) if no output file was specified. The remaining lines contain the command-line arguments, one per line, in the order they appear. These do not include regular pandoc options and their arguments, but do include any options appearing after a separator at the end of the line.

Ignore command-line arguments (for use in wrapper scripts). Regular pandoc options are not ignored. Thus, for example,

is equivalent to

Templates

When the option is used, pandoc uses a template to add header and footer material that is needed for a self-standing document. To see the default template that is used, just type

where FORMAT is the name of the output format. A custom template can be specified using the option. You can also override the system default templates for a given output format FORMAT by putting a file in the user data directory (see , above). Exceptions:

  • For output, customize the template.
  • For output, customize the template (or the template, if you use , or the template, if you use , or the template, if you use ).
  • has no template (however, you can use to customize the output).

Templates contain variables, which allow for the inclusion of arbitrary information at any point in the file. Variables may be set within the document using YAML metadata blocks. They may also be set at the command line using the option: variables set in this way override metadata fields with the same name.

Variables set by pandoc

Some variables are set automatically by pandoc. These vary somewhat depending on the output format, but include metadata fields as well as the following:

,

source and destination filenames, as given on the command line. can also be a list if input comes from multiple files, or empty if input is from stdin. You can use the following snippet in your template to distinguish them:

Similarly, can be if output goes to the terminal.

, ,

allow identification of basic aspects of the document. Included in PDF metadata through LaTeX and ConTeXt. These can be set through a pandoc title block, which allows for multiple authors, or through a YAML metadata block:

document subtitle, included in HTML, EPUB, LaTeX, ConTeXt, and Word docx; renders in LaTeX only when using a document class that supports , such as or the KOMA-Script series (, , ).1
author affiliations (in LaTeX and Beamer only). Can be a list, when there are multiple authors.
document summary, included in LaTeX, ConTeXt, AsciiDoc, and Word docx
list of keywords to be included in HTML, PDF, and AsciiDoc metadata; may be repeated as for , above
contents specified by (may have multiple values)
non-null value if was specified
title of table of contents (works only with EPUB, opendocument, odt, docx, pptx)
contents specified by (may have multiple values)
contents specified by (may have multiple values)
body of document
JSON representation of all of the document’s metadata. Field values are transformed to the selected output format.

Language variables

identifies the main language of the document, using a code according to BCP 47 (e.g. or ). For some output formats, pandoc will convert it to an appropriate format stored in the additional variables , (LaTeX) and (ConTeXt).

Native pandoc Spans and Divs with the lang attribute (value in BCP 47) can be used to switch the language in that range. In LaTeX output, and variables will be generated automatically based on the attributes of Spans and Divs in the document.

the base direction of the document, either (right-to-left) or (left-to-right).

For bidirectional documents, native pandoc s and s with the attribute (value or ) can be used to override the base direction in some output formats. This may not always be necessary if the final renderer (e.g. the browser, when generating HTML) supports the Unicode Bidirectional Algorithm.

When using LaTeX for bidirectional documents, only the engine is fully supported (use ).

Variables for slides

Variables are available for producing slide shows with pandoc, including all reveal.js configuration options.

title graphic for Beamer documents
logo for Beamer documents
base URL for Slidy documents (defaults to )
base URL for Slideous documents (defaults to )
base URL for S5 documents (defaults to )
base URL for reveal.js documents (defaults to )
, , , ,
themes for LaTeX documents
options for LaTeX beamer themes (a list).
controls navigation symbols in documents (default is for no navigation symbols; other valid values are , , and ).
enables on “title pages” for new sections in documents (default = true).
when true, the package is loaded (for producing an article from beamer slides).
aspect ratio of slides (for beamer only, for 16:10, for 16:9, for 14:9, for 1.41:1, for 5:4, for 4:3 which is the default, and for 3:2).

Variables for LaTeX

LaTeX variables are used when creating a PDF.

paper size, e.g. ,
font size for body text (e.g. , )
document class, e.g. , , ,
option for document class, e.g. ; may be repeated for multiple options
option for package, e.g. ; may be repeated for multiple options
, , ,
sets margins, if is not used (otherwise overrides these)
adjusts line spacing using the package, e.g. ,
font package for use with : TeX Live includes many options, documented in the LaTeX Font Catalogue. The default is Latin Modern.
options for package used as : e.g. with set to provides Palatino with old-style figures and true small caps; may be repeated for multiple options
, , , ,
font families for use with or : take the name of any system font, using the package. Note that if is used, the package must be available.
, , , ,
options to use with , , , , in and . Allow for any choices available through , such as the OpenType features . May be repeated for multiple options.
allows font encoding to be specified through package (with ); default is (see guide to LaTeX font encodings)
options to pass to the microtype package
add color to link text; automatically enabled if any of , , , or are set
, , ,
color for internal links, citation links, external links, and links in table of contents: uses options allowed by , including the , , and lists
causes links to be printed as footnotes
uses document class settings for indentation (the default LaTeX template otherwise removes indentation and adds space between paragraphs)
disables default behavior of LaTeX template that redefines (sub)paragraphs as sections, changing the appearance of nested headings in some classes
specifies contents of acknowledgments footnote after document title.
include table of contents (can also be set using )
level of section to include in table of contents
numbering depth for sections, if sections are numbered
,
include list of figures, list of tables
bibliography to use for resolving references
bibliography style, when used with and .
bibliography title, when used with and .
list of options for biblatex.
list of options for natbib.
An option for LaTeX’s . The default article class supports ‘plain’ (default), ‘empty’, and ‘headings’; headings puts section titles in the header.

Variables for ConTeXt

paper size, e.g. , , (see ConTeXt Paper Setup); may be repeated for multiple options
options for page margins and text arrangement (see ConTeXt Layout); may be repeated for multiple options
, , ,
sets margins, if is not used (otherwise overrides these)
font size for body text (e.g. , )
, , ,
font families: take the name of any system font (see ConTeXt Font Switching)
,
color for links outside and inside a page, e.g. , (see ConTeXt Color)
typeface style for links, e.g. , , , , , ,
controls indentation of paragraphs, e.g. (see ConTeXt Indentation); may be repeated for multiple options
spacing between paragraphs, e.g. , (using )
adjusts line spacing, e.g. (using ); may be repeated for multiple options
,
text to be placed in running header or footer (see ConTeXt Headers and Footers); may be repeated up to four times for different placement
page number style and location (using ); may be repeated for multiple options
include table of contents (can also be set using )
,
include list of figures, list of tables

Variables for man pages

section number in man pages
header in man pages
footer in man pages
adjusts text to left (), right (), center (), or both () margins
if (the default), hyphenation will be used

Variables for ms

point size (e.g. )
line height (e.g. )
font family (e.g. or )
paragraph indent (e.g. )

Using variables in templates

Variable names are sequences of alphanumerics, , and , starting with a letter. A variable name surrounded by signs will be replaced by its value. For example, the string in

will be replaced by the document title.

To write a literal in a template, use .

Templates may contain conditionals. The syntax is as follows:

This will include in the template if has a non-null value; otherwise it will include . and are placeholders for any valid template text, and may include interpolated variables or other conditionals. The section may be omitted.

When variables can have multiple values (for example, in a multi-author document), you can use the keyword:

You can optionally specify a separator to be used between consecutive items:

A dot can be used to select a field of a variable that takes an object as its value. So, for example:

If you use custom templates, you may need to revise them as pandoc changes. We recommend tracking the changes in the default templates, and modifying your custom templates accordingly. An easy way to do this is to fork the pandoc-templates repository and merge in changes after each pandoc release.

Templates may contain comments: anything on a line after will be treated as a comment and ignored.

Extensions

The behavior of some of the readers and writers can be adjusted by enabling or disabling various extensions.

An extension can be enabled by adding to the format name and disabled by adding . For example, is strict Markdown with footnotes enabled, while is pandoc’s Markdown without footnotes or pipe tables.

The markdown reader and writer make by far the most use of extensions. Extensions only used by them are therefore covered in the section Pandoc’s Markdown below (See Markdown variants for and .) In the following, extensions that also work for other formats are covered.

Typography

Extension:

Interpret straight quotes as curly quotes, as em-dashes, as en-dashes, and as ellipses. Nonbreaking spaces are inserted after certain abbreviations, such as “Mr.”

This extension can be enabled/disabled for the following formats:

input formats
, , , , , ,
output formats
, , ,
enabled by default in
, , (both input and output)

Note: If you are writing Markdown, then the extension has the reverse effect: what would have been curly quotes comes out straight.

In LaTeX, means to use the standard TeX ligatures for quotation marks ( and for double quotes, and for single quotes) and dashes ( for en-dash and for em-dash). If is disabled, then in reading LaTeX pandoc will parse these characters literally. In writing LaTeX, enabling tells pandoc to use the ligatures when possible; if is disabled pandoc will use unicode quotation mark and dash characters.

Headers and sections

Extension:

A header without an explicitly specified identifier will be automatically assigned a unique identifier based on the header text.

This extension can be enabled/disabled for the following formats:

input formats
, , , ,
output formats
,
enabled by default in
,

The algorithm used to derive the identifier from the header text is:

  • Remove all formatting, links, etc.
  • Remove all footnotes.
  • Remove all punctuation, except underscores, hyphens, and periods.
  • Replace all spaces and newlines with hyphens.
  • Convert all alphabetic characters to lowercase.
  • Remove everything up to the first letter (identifiers may not begin with a number or punctuation mark).
  • If nothing is left after this, use the identifier .

Thus, for example,

These rules should, in most cases, allow one to determine the identifier from the header text. The exception is when several headers have the same text; in this case, the first will get an identifier as described above; the second will get the same identifier with appended; the third with ; and so on.

These identifiers are used to provide link targets in the table of contents generated by the option. They also make it easy to provide links from one section of a document to another. A link to this section, for example, might look like this:

Note, however, that this method of providing links to sections works only in HTML, LaTeX, and ConTeXt formats.

If the option is specified, then each section will be wrapped in a (or a , if was specified), and the identifier will be attached to the enclosing (or ) tag rather than the header itself. This allows entire sections to be manipulated using JavaScript or treated differently in CSS.

Extension:

Causes the identifiers produced by to be pure ASCII. Accents are stripped off of accented Latin letters, and non-Latin letters are omitted.

Math Input

The extensions , , and are described in the section about Pandoc’s Markdown.

However, they can also be used with HTML input. This is handy for reading web pages formatted using MathJax, for example.

Raw HTML/TeX

The following extensions (especially how they affect Markdown input/output) are also described in more detail in their respective sections of Pandoc’s Markdown.

Extension:

When converting from HTML, parse elements to raw HTML which are not representable in pandoc’s AST. By default, this is disabled for HTML input.

Extension:

Allows raw LaTeX, TeX, and ConTeXt to be included in a document.

This extension can be enabled/disabled for the following formats (in addition to ):

input formats
, ,
output formats

Extension:

This extension is enabled by default for HTML input. This means that s are parsed to pandoc native elements. (Alternatively, you can parse them to raw HTML using .)

When converting HTML to Markdown, for example, you may want to drop all s and s:

Extension:

Analogous to above.

Literate Haskell support

Extension:

Treat the document as literate Haskell source.

This extension can be enabled/disabled for the following formats:

input formats
, ,
output formats
, , ,

If you append (or ) to one of the formats above, pandoc will treat the document as literate Haskell source. This means that

  • In Markdown input, “bird track” sections will be parsed as Haskell code rather than block quotations. Text between and will also be treated as Haskell code. For ATX-style headers the character ‘=’ will be used instead of ‘#’.

  • In Markdown output, code blocks with classes and will be rendered using bird tracks, and block quotations will be indented one space, so they will not be treated as Haskell code. In addition, headers will be rendered setext-style (with underlines) rather than ATX-style (with ‘#’ characters). (This is because ghc treats ‘#’ characters in column 1 as introducing line numbers.)

  • In restructured text input, “bird track” sections will be parsed as Haskell code.

  • In restructured text output, code blocks with class will be rendered using bird tracks.

  • In LaTeX input, text in environments will be parsed as Haskell code.

  • In LaTeX output, code blocks with class will be rendered inside environments.

  • In HTML output, code blocks with class will be rendered with class and bird tracks.

Examples:

reads literate Haskell source formatted with Markdown conventions and writes ordinary HTML (without bird tracks).

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