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`.
`order`	Order for document when included in a website automatic sidebar menu.

Format Options

quarto-required

A semver version range describing the supported quarto versions for this document or project.

Examples:

>= 1.1.0: Require at least quarto version 1.1
1.*: Require any quarto versions whose major version number is 1

preview-mode

The mode to use when previewing this document. To disable any special previewing features, pass raw as the preview-mode.

Numbering

`number-sections`	Number section headings rendered output. 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.

Layout

grid

Properties of the grid system used to layout Quarto HTML pages.

Code

code-annotations

The style to use when displaying code annotations. Set this value to false to hide code annotations.

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). `true` (default): evaluate code cell `false`: don’t evaluate code cell `[...]`: A list of positive or negative line numbers to selectively include or exclude lines (explicit inclusion/excusion of lines is available only when using the knitr engine)
`echo`	Include cell source code in rendered output. `true` (default in most formats): include source code in output `false` (default in presentation formats like `beamer`, `revealjs`, and `pptx`): do not include source code in output `fenced`: in addition to echoing, include the cell delimiter as part of the output. `[...]`: A list of positive or negative line numbers to selectively include or exclude lines (explicit inclusion/excusion of lines is available only when using the knitr engine)
`output`	Include the results of executing the code in the output. Possible values: `true`: Include results. `false`: Do not include results. `asis`: Treat output as raw markdown with no enclosing containers.
`warning`	Include 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). `true`: Cache results `false`: Do not cache results `refresh`: Force a refresh of the cache even if has not been otherwise invalidated.
`freeze`	Control the re-use of previous computational output when rendering. `true`: Never recompute previously generated computational output during a global project render `false` (default): Recompute previously generated computational output `auto`: Re-compute previously generated computational output only in case their source file changes

Figures

`fig-width`	Default width for figures generated by Matplotlib or R graphics. Note that with the Jupyter engine, this option has no effect when provided at the cell level; it can only be provided with document or project metadata.
`fig-height`	Default height for figures generated by Matplotlib or R graphics. Note that with the Jupyter engine, this option has no effect when provided at the cell level; it can only be provided with document or project metadata.
`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. Note that with the Jupyter engine, this option has no effect when provided at the cell level; it can only be provided with document or project metadata.
`fig-asp`	The aspect ratio of the plot, i.e., the ratio of height/width. When `fig-asp` is specified, the height of a plot (the option `fig-height`) is calculated from `fig-width * fig-asp`. The `fig-asp` option is only available within the knitr engine.

Tables

df-print

Method used to print tables in Knitr engine documents:

default: Use the default S3 method for the data frame.
kable: Markdown table using the knitr::kable() function.
tibble: Plain text table using the tibble package.
paged: HTML table with paging for row and column overflow.

The default printing method is kable.

Links

notebook-subarticles

Controls the display of links to notebooks that provided embedded content or are created from documents.

Defaults to true - specify false to disable embedding Notebook as subarticles with the JATS output.

References

`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" } } }`

Crossrefs

crossref

Configuration for crossref labels and prefixes.

Citation

citation

Citation information for the document itself specified as CSL YAML in the document front matter.

For more on supported options, see Citation Metadata.

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 (rtl or ltr).

For bidirectional documents, native pandoc spans and divs with the dir attribute 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.

Metadata

copyright

The copyright for this document, if any.

license

The license for this document, if any.

Creative Commons licenses CC BY, CC BY-SA, CC BY-ND, CC BY-NC, CC BY-NC-SA, and CC BY-NC-ND will automatically generate a license link in the document appendix. Other license text will be placed in the appendix verbatim.

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.
`template-partials`	Include the specified files as partials accessible to the template for the generated content.
`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.
`shortcodes`	Specify Lua scripts that implement shortcode handlers
`keep-md`	Keep the markdown file generated by executing code
`keep-ipynb`	Keep the notebook file generated from executing code.
`ipynb-filters`	Filters to pre-process ipynb files before rendering to markdown
`ipynb-shell-interactivity`	Specify which nodes should be run interactively (displaying output from expressions)
`plotly-connected`	If true, use the “notebook_connected” plotly renderer, which downloads its dependencies from a CDN and requires an internet connection to view.
`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.
`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.
`html-table-processing`	If `none`, do not process tables in HTML input.

Text Output

`wrap`	Determine how text is wrapped in the output (the source code, not the rendered version). `auto` (default): Pandoc will attempt to wrap lines to the column width specified by `columns` (default 72). `none`: Pandoc will not wrap lines at all. `preserve`: Pandoc will attempt to preserve the wrapping from the source document. 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. For `typst`, number of columns for body text.
`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`: Use Windows line endings `lf`: Use macOS/Linux/UNIX line endings `native` (default): Use line endings appropriate to the OS on which pandoc is being run).