roxygen2

Basic documentation

Action	Code	Details
Title	@title Title here
Description	@description Description here
Parameter	@param data The dataset
Dot parameters	@param ... Additional arguments
Return	@return Return value description here
Class slot	@slot slotName Description here
Details	@details Details here
Note	@note Notes here
Data format	@format Format description here

Text formatting

Action	Code	Details
Enable markdown	@md
Emphasis	_wow_
Bold	*wow*
In-line equation	\eqn{a + b}
Display equation	\deqn{a + b}
Code	`mu <- mean(data)`
Code	\code{mu <- mean(data)}
Code block	mu <- mean(data)
Monospace font (looks like code)	\preformatted{ text }
Package name	\pkg{stats}
Unordered list	\itemize{ \item Option A \item Option B }
Ordered list	\enumerate{ \item First item \item Second item }
Named list	\describe{ \item{Opt A}{Describe option A}< \item{Opt B}{Describe option B} }
Table	?	Use markdown?
Sections	@details First part @details Second part (will be a new section)
Arbitrary sections	@section Title: Text here
Subsections	@details ## This is a subsection With text #### Subsubsection here With text

Link

Action	Code	Details
Website	<https://r-project.org>
With different text	[text](link)
To internal topic defined by @name name	[name]
To external package	[stats][stats-package]
To external package function	[stats::predict]
To internal or global function	[predict()]
To package function	[stats::predict()]
To function with different text	[fancyName()][stats::predict()]
To class	[Time]
To external class	[stats::Time]
To S4 class	\linkS4class{lcModel}
With special characters	\code{\link[magrittr]{\%>\%}}
See-also	@seealso [mean] [stats::median]
See-also vignette	@seealso browseVignettes('roxygen2')
Family	@family sharedNames
Specify source	@source This dataset was generated using [generateData]
References	@references \insertRef{benaglia2009mixtools}{latrend}
E-mail	\email{example@@example.com}

Examples

Documenting code examples

Action	Code	Details
Examples	@examples 1 + 1 mean(1:9)
Examples that should not be run	@examples 1 + 1 \dontrun{ stop('oops') }
Examples that should not be tested	@examples \donttest{ stop('oops') }
Examples for interactive usage only	@examples if interactive() browseURL("https://roxygen2.r-lib.org")

Dynamic content

Action	Code	Details
In-line code evaluation	`r getRversion()`	Evaluated during every roxygenize call
Code block evaluation	```{r} 1 + 1 </td> <td markdown="1">Code blocks cannot refer to each other</td> </tr> <tr markdown="1"> <td markdown="1"> Generate figure </td> <td> ```R ```{r iris-pairs-plot} pairs(iris[1:4])[unclass(iris$Species)]) </td> <td markdown="1"></td> </tr> <tr markdown="1"> <td markdown="1"> Dynamic documentation </td> <td> ```R 

Generating documentation

Action	Code	Details
Generate docs	roxygen2::roxygenise()	Ctrl+Shift+D
Clean files, then generate docs	roxygen2::roxygenise(clean = TRUE)

Topics

Action	Code	Details
Don't generate topic	@noRd
Create stand-alone topic	@name docname @title Topic title NULL
Package topic	@details Package documentation here. @keywords internal "_PACKAGE"
Topic name	@name simpleName
Topic file name	@rdname simpleName
Specify doc inclusion order	@order 1	Then @order 2 for the second doc
Define alias	@aliases shortName
Define alias for S4 method	@aliases predictForCluster,lcModel-method
Inherit doc	@inherit docName
Inherit doc components	@inherit docName details return
Inherit section	@inheritSection docName Section title
Inherit param descriptions from another internal function	@inheritParams internalFun
Inherit param descriptions from an external function	@inheritParams stats::predict
Inherit dot parameters	@inheritDotParams
Hide documentation	@keywords internal

Namespace generation

Action	Code	Details
Import package	@import stats
Import packages	@import stats splines
Import function(s) from package	@importFrom stats predict fitted
Import S3 generic	@importFrom pkg generic
Import S4 classes from package	@importClassesFrom stats Time
Import S4 methods from package	@importMethodsFrom stats time time2
Collate / ensure other R files are loaded first	@include first.R second.R
Export function	@export
Export class and methods	@export setClass(…)
Export class	@exportClass lcModel
Export class method	@exportMethod evaluate