Write R Documentation in Markdown

Gábor Csárdi



Starting from version 6.0.0, roxygen supports markdown markup within most roxygen tags. Roxygen uses the commonmark package, which is based on the CommonMark Reference Implementation to parse these tags. See http://commonmark.org/help/ for more about the parser and the markdown language it supports.

Turning on markdown support

There are two ways to turn on markdown support for a package: globally, at the package level, and locally at the block level.

To turn on markdown for the whole package, insert this entry into the DESCRIPTION file of the package:

Roxygen: list(markdown = TRUE)

The position of the entry in the file does not matter. After this, all Roxygen documentation will be parsed as markdown.

Alternatively, you can use the @md tag to turn on markdown support for a single documentation chunk. This is a good option to write any new documentation for existing packages in markdown.

There is also a new @noMd tag. Use this if you turned on markdown parsing globally, but need to avoid it for a single chunk. This tag is handy if the markdown parser interferes with more complex Rd syntax.

Here is an example roxygen chunk that uses markdown.

#' Use roxygen to document a package.
#' This function is a wrapper for the [roxygen2::roxygenize()] function from
#' the `roxygen2` package. See the documentation and vignettes of
#' that package to learn how to use roxygen.
#' @param pkg package description, can be path or package name.  See
#'   [as.package()] for more information
#' @param clean,reload Deprecated.
#' @inheritParams roxygen2::roxygenise
#' @seealso [roxygen2::roxygenize()], `browseVignettes("roxygen2")`
#' @export
#' @md



Emphasis and strong (bold) text are supported. For emphasis, put the text between asterisks or underline characters. For strong text, use two asterisks at both sides.


Inline code is supported via backticks.

For blocks of code, put your code between triple backticks:

Note that this is not needed in @examples, since its contents is formatted as R code, anyway.


Regular Markdown lists are recognized and converted to \enumerate{} or \itemize{} lists:

Nested lists are also supported.

Note that you do not have leave an empty line before the list. This is different from some markdown parsers.


The parser recognizes the markdown notation for embedded images. The image files must in the man/figures directory:

Roxygen and Rd tags not parsed as markdown

Some of the roxygen tags are not parsed as markdown. Most of these are unlikely to contain text that needs markup, so this is not an important restriction. Tags without markdown support: @aliases, @backref, @docType, @encoding, @evalRd, @example, @examples, @family, @inheritParams, @keywords, @method @name, @md, @noMd, @noRd, @rdname, @rawRd, @usage.

When mixing Rd and markdown notation, most Rd tags may contain markdown markup, the ones that can not are: \acronym, \code, \command, \CRANpkg, \deqn, \doi, \dontrun, \dontshow, \donttest, \email, \env, \eqn, \figure, \file, \if, \ifelse, \kbd, \link, \linkS4class, \method, \newcommand, \option, \out, \packageAuthor, \packageDescription, \packageDESCRIPTION, \packageIndices, \packageMaintainer, \packageTitle, \pkg, \PR, \preformatted, \renewcommand, \S3method, \S4method, \samp, \special, \testonly, \url, \var, \verb.

Possible problems

Mixing markdown and Rd markup

Note that turning on markdown does not turn off the standard Rd syntax. We suggest that you use the regular Rd tags in a markdown roxygen chunk only if necessary. The two parsers do occasionally interact, and the markdown parser can pick up and reformat Rd syntax, causing an error, or corrupted manuals.

Leading whitespace

Leading whitespace is interpreted by the commonmark parser, whereas it is ignored by the Rd parser (except in \preformatted{}). Make sure that you only include leading whitespace intentionally, for example for nested lists.

Spurious lists

The Commonmark parser does not require an empty line before lists, and this might lead to unintended lists if a line starts with a number followed by a dot, or with an asterisk followed by whitespace: