JATS Options

JATS (Journal Article Tag Suite) is an XML format for marking up and exchanging journal content. You can learn more about JATS here https://jats.nlm.nih.gov/publishing/.

format: jats
format: jats_archiving
format: jats_articleauthoring
format: jats_publishing

Title & Author

title

Document title

date

Document date

author

Author or authors of the document

affiliation

The list of organizations with which contributors are affiliated. Each institution is added as an [<aff>] element to the author’s contrib-group. See the Pandoc JATS documentation for details on affiliation fields.

copyright

Licensing and copyright information. This information is rendered via the <permissions> element. The variables type, link, and text should always be used together. See the Pandoc JATS documentation for details on copyright fields.

article

Information concerning the article that identifies or describes it. The key-value pairs within this map are typically used within the <article-meta> element. See the Pandoc JATS documentation for details on article fields.

journal

Information on the journal in which the article is published. See the Pandoc JATS documentation for details on journal fields.

abstract

Summary of document

notes

Additional notes concerning the whole article. Added to the article’s frontmatter via the <notes> element.

tags

List of keywords. Items are used as contents of the <kwd> element; the elements are grouped in a <kwd-group> with the kwd-group-type value author.

Numbering

number-sections

Number section headings rendered ouptut. By default, sections are not numbered. Sections with class .unnumbered will never be numbered, even if number-sections is specified.

number-offset

Offset for section headings in output (offsets are 0 by default) The first number is added to the section number for top-level headings, the second for second-level headings, and so on. So, for example, if you want the first top-level heading in your document to be numbered “6”, specify number-offset: 5. If your document starts with a level-2 heading which you want to be numbered “1.5”, specify number-offset: [1,4]. Implies number-sections

shift-heading-level-by

Shift heading levels by a positive or negative integer. For example, with shift-heading-level-by: -1, level 2 headings become level 1 headings, and level 3 headings become level 2 headings. Headings cannot have a level less than 1, so a heading that would be shifted below level 1 becomes a regular paragraph. Exception: with a shift of -N, a level-N heading at the beginning of the document replaces the metadata title.

Execution

Execution options should be specified within the execute key. For example:

execute:
  echo: false
  warning: false
eval

Evaluate code cells (if false just echos the code into output).

echo

Include cell source code in rendered output. Specify fenced to include the cell delimiter as part of the output.

output

Include the results of executing the code in the output (specify asis to treat output as raw markdown with no enclosing containers).

warning

Including warnings in rendered output.

error

Include errors in the output (note that this implies that errors executing code will not halt processing of the document).

include

Catch all for preventing any output (code or results) from being included in output.

cache

Cache results of computations (using the knitr cache for R documents, and Jupyter Cache for Jupyter documents).

Note that cache invalidation is triggered by changes in chunk source code (or other cache attributes you’ve defined). Use refresh to force a refresh of the cache even if has not been otherwise invalidated.

freeze

Option to denote that computational documents should never be re-rendered during a global project render (freeze: true), or alternatively only be re-rendered when their source file changes (freeze: auto).

Figures

fig-width

Default width for figures generated by Matplotlib or R graphics

fig-height

Default height for figures generated by Matplotlib or R graphics

fig-format

Default format for figures generated by Matplotlib or R graphics (retina, png, jpeg, svg, or pdf)

fig-dpi

Default DPI for figures generated by Matplotlib or R graphics

Tables

tbl-colwidths

Apply explicit table column widths for markdown grid tables and pipe tables that are more than columns characters wide (72 by default).

Some formats (e.g. HTML) do an excellent job automatically sizing table columns and so don’t benefit much from column width specifications. Other formats (e.g. LaTeX) require table column sizes in order to correctly flow longer cell content (this is a major reason why tables > 72 columns wide are assigned explicit widths by Pandoc).

This can be specified as:

  • auto: Apply markdown table column widths except when there is a hyperlink in the table (which tends to throw off automatic calculation of column widths based on the markdown text width of cells). (auto is the default for HTML output formats)

  • true: Always apply markdown table widths (true is the default for all non-HTML formats)

  • false: Never apply markdown table widths.

  • [40,30,30]: Array of explicit width percentages.

Citations

bibliography

Document bibliography (BibTeX or CSL). May be a single file or a list of files

csl

Citation Style Language file to use for formatting references.

citeproc

Turn on built-in citation processing. To use this feature, you will need to have a document containing citations and a source of bibliographic data: either an external bibliography file or a list of references in the document’s YAML metadata. You can optionally also include a csl citation style file.

citation-abbreviations

JSON file containing abbreviations of journals that should be used in formatted bibliographies when form="short" is specified. The format of the file can be illustrated with an example:

{ "default": {
    "container-title": {
      "Lloyd's Law Reports": "Lloyd's Rep",
      "Estates Gazette": "EG",
      "Scots Law Times": "SLT"
    }
  }
}

Language

lang

Identifies the main language of the document using IETF language tags (following the BCP 47 standard), such as en or en-GB. The Language subtag lookup tool can look up or verify these tags.

This affects most formats, and controls hyphenation in PDF output when using LaTeX (through babel and polyglossia) or ConTeXt.

language

YAML file containing custom language translations

dir

The base script direction for the document.

For bidirectional documents, native pandoc spans and divs with the dir attribute (value rtl or ltr) 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 xelatex engine is fully supported (use --pdf-engine=xelatex).

Includes

metadata-files

Read metadata from the supplied YAML (or JSON) files. This option can be used with every input format, but string scalars in the YAML file will always be parsed as Markdown. Generally, the input will be handled the same as in YAML metadata blocks. Values in files specified later in the list will be preferred over those specified earlier. Metadata values specified inside the document, or by using -M, overwrite values specified with this option.

Rendering

from

Format to read from. Extensions can be individually enabled or disabled by appending +EXTENSION or -EXTENSION to the format name (e.g. markdown+emoji).

output-file

Output file to write to

output-ext

Extension to use for generated output file

template

Use the specified file as a custom template for the generated document.

standalone

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

filters

Specify executables or Lua scripts to be used as a filter transforming the pandoc AST after the input is parsed and before the output is written.

keep-md

Keep the markdown file generated by executing code

keep-ipynb

Keep the notebook file generated from executing code.

extract-media

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. Media are downloaded, read from the file system, or extracted from a binary container (e.g. docx), as needed. The original file paths are used if they are relative paths not containing … Otherwise filenames are constructed from the SHA1 hash of the contents.

resource-path

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.

default-image-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.

abbreviations

Specifies a custom abbreviations file, with abbreviations one to a line. This list is used when reading Markdown input: strings found in this list will be followed by a nonbreaking space, and the period will not produce sentence-ending space in formats like LaTeX. The strings may not contain spaces.

dpi

Specify the default dpi (dots per inch) value for conversion from pixels to inch/ centimeters and vice versa. (Technically, the correct term would be ppi: pixels per inch.) The default is 96. When images contain information about dpi internally, the encoded value is used instead of the default specified by this option.

Text Output

wrap

Determine how text is wrapped in the output (the source code, not the rendered version). With auto (the default), pandoc will attempt to wrap lines to the column width specified by columns (default 72). With none, pandoc will not wrap lines at all. With preserve, 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

columns

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

tab-stop

Specify the number of spaces per tab (default is 4). Note that tabs within normal textual input are always converted to spaces. Tabs within code are also converted, however this can be disabled with preserve-tabs: false.

preserve-tabs

Preserve tabs within code instead of converting them to spaces. (By default, pandoc converts tabs to spaces before parsing its input.) Note that this will only affect tabs in literal code spans and code blocks. Tabs in regular text are always treated as spaces.

eol

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