Rd (documentation) tags

Basics

A roxygen block is a sequence of lines starting with #' (optionally preceded by whitespace). The first lines of the block forms the description, described next. The description continues until the first tag. Tags start with @, like @details or @param , and must appear at the beginning of a line. The content of a tag extends to the start of the next tag or the end of the block. Text within the description or tags can be formatted using Markdown or Rd commands; see vignette("rd-formatting") for details.

A block continues until it hits R code, typically a function or object assignment. Blocks ignore empty lines, including lines made up of non-roxygen comments. If you need to separate two blocks, use NULL.

The description block

Each documentation block starts with some text which defines the title, the description, and the details. Here’s an example showing what the documentation for sum() might look like if it had been written with roxygen:

#' Sum of vector elements
#'
#' `sum` returns the sum of all the values present in its arguments.
#'
#' This is a generic function: methods can be defined for it directly
#' or via the [Summary()] group generic. For this to work properly,
#' the arguments `...` should be unnamed, and dispatch is on the
#' first argument.
sum <- function(..., na.rm = TRUE) {}

This introductory block is broken up as follows:

You can also use explicit @title, @description, and @details tags. This is unnecessary unless you want to have a multi-paragraph description, bulleted list, or other more exotic structure.

#' Sum of vector elements
#' 
#' @description
#' `sum` returns the sum of all the values present in its arguments.
#'
#' @details
#' This is a generic function: methods can be defined for it directly
#' or via the [Summary()] group generic. For this to work properly,
#' the arguments `...` should be unnamed, and dispatch is on the
#' first argument.

Object specifics

Further details of roxygen2 depend on what you’re documenting. The following sections describe the most commonly used tags for functions, S3, S4, datasets, and packages.

Functions

Functions are the mostly commonly documented objects. Most functions use three tags:

We could use these new tags to improve our documentation of sum() as follows:

#' Sum of vector elements
#'
#' `sum()` returns the sum of all the values present in its arguments.
#'
#' This is a generic function: methods can be defined for it directly
#' or via the [Summary] group generic. For this to work properly,
#' the arguments `...` should be unnamed, and dispatch is on the
#' first argument.
#'
#' @param ... Numeric, complex, or logical vectors.
#' @param na.rm A logical scalar. Should missing values (including `NaN`)
#'   be removed?
#' @return If all inputs are integer and logical, then the output
#'   will be an integer. If integer overflow 
#'   (<http://en.wikipedia.org/wiki/Integer_overflow>) occurs, the output
#'   will be NA with a warning. Otherwise it will be a length-one numeric or
#'   complex vector.
#'
#'   Zero-length vectors have sum 0 by definition. See
#'   <http://en.wikipedia.org/wiki/Empty_sum> for more details.
#' @examples
#' sum(1:10)
#' sum(1:5, 6:10)
#' sum(F, F, F, T, T)
#'
#' sum(.Machine$integer.max, 1L)
#' sum(.Machine$integer.max, 1)
#'
#' \dontrun{
#' sum("a")
#' }
sum <- function(..., na.rm = TRUE) {}

Indent the second and subsequent lines of a tag so that when scanning the documentation so it’s easy to see where one tag ends and the next begins. Tags that always span multiple lines (like @example) should start on a new line and don’t need to be indented.

In most case, the function usage will be automatically derived from the function specification. For the cases where it is not, please file an issue and use @usage to override the default with you want. If you want to suppress the usage altogether (which is sometimes useful for internal or deprecated functions), you can use @usage NULL.

S3

S4

S4 generics are also functions, so document them as such.

Document S4 classes by adding a roxygen block before setClass(). Use @slot to document the slots of the class. Here’s a simple example:

#' An S4 class to represent a bank account
#'
#' @slot balance A length-one numeric vector
Account <- setClass("Account",
  slots = list(balance = "numeric")
)

S4 methods are a little more complicated. Unlike S3 methods, all S4 methods must be documented. You can document them in three places:

Use either @rdname or @describeIn to control where method documentation goes. See the next section for more details.

R6

Starting from version 7.0.0 roxygen treats documentation for R6 classes specially:

Roxygen2 automatically generates additional sections for an R6 class:

An example from the R6 tutorial:

#' R6 Class Representing a Person
#'
#' @description
#' A person has a name and a hair color.
#'
#' @details
#' A person can also greet you.

Person <- R6::R6Class("Person",
public = list(

    #' @field name First or full name of the person.
    name = NULL,

    #' @field hair Hair color of the person.
    hair = NULL,

    #' @description
    #' Create a new person object.
    #' @param name Name.
    #' @param hair Hair color.
    #' @return A new `Person` object.
    initialize = function(name = NA, hair = NA) {
      self$name <- name
      self$hair <- hair
      self$greet()
    },

    #' @description
    #' Change hair color.
    #' @param val New hair color.
    #' @examples
    #' P <- Person("Ann", "black")
    #' P$hair
    #' P$set_hair("red")
    #' P$hair
    set_hair = function(val) {
      self$hair <- val
    },

    #' @description
    #' Say hi.
    greet = function() {
      cat(paste0("Hello, my name is ", self$name, ".\n"))
    }
  )
)

Datasets

Datasets are usually stored as .rdata files in data/ and not as regular R objects in the package. This means you need to document them slightly differently: instead of documenting the data directly, you quote the dataset’s name.

#' Prices of 50,000 round cut diamonds
#'
#' A dataset containing the prices and other attributes of almost 54,000
#' diamonds.
#'
#' @format A data frame with 53940 rows and 10 variables
#' \describe{
#'   \item{price}{price in US dollars (\$326--\$18,823)}
#'   \item{carat}{weight of the diamond (0.2--5.01)}
#'   \item{cut}{quality of the cut (Fair, Good, Very Good, Premium, Ideal)}
#'   \item{color}{diamond colour, from D (best) to J (worst)}
#'   \item{clarity}{a measurement of how clear the diamond is (I1 (worst), SI2,
#'     SI1, VS2, VS1, VVS2, VVS1, IF (best))}
#'   \item{x}{length in mm (0--10.74)}
#'   \item{y}{width in mm (0--58.9)}
#'   \item{z}{depth in mm (0--31.8)}
#'   \item{depth}{total depth percentage = z / mean(x, y) = 2 * z / (x + y) (43--79)}
#'   \item{table}{width of top of diamond relative to widest point (43--95)}
#' }
#' @source <http://www.diamondse.info/>
"diamonds"
#> [1] "diamonds"

Note the use of two additional tags that are particularly useful for documenting data:

Packages

As well as documenting every object inside the package, you can also document the package itself by documenting the special sentinel "_PACKAGE". We recommend placing package documentation in {pkgname}-package.R, and have @keywords internal. Here’s an example:

#' @details
#' The only function you're likely to need from roxygen2 is [roxygenize()]. 
#' Otherwise refer to the vignettes to see how to format the documentation.
#' @keywords internal
"_PACKAGE"

Package documentation is a good place to put @section Package options: that documents options used by the package.

Some notes:

Sections

You can add arbitrary sections with the @section tag. This is a useful way of breaking a long details section into multiple chunks with useful headings. Section titles should be in sentence case, must fit on one line, and must be followed by a colon.

#' @section Warning:
#' Do not operate heavy machinery within 8 hours of using this function.

You can also create sections using the Markdown syntax for headers. For example, the previously-defined section can be created with Markdown headers like this:

#' @details # Warning
#' Do not operate heavy machinery within 8 hours of using this function.

Note that ‘#’ may only appear after the @description and @details tags. Since @details can appear multiple times in a block, you can always precede a ‘#’ section with @details.

To add a subsection, use level two or greater headings:

#' @details # Warning
#' You must not call this function unless ...
#'
#' ## Exceptions
#' Apart from the following special cases...

If you find yourself adding a lot of sections, you might consider using a vignette instead.

Do repeat yourself

There is tension between the DRY (do not repeat yourself) principle of programming and the need for documentation to be self-contained. It’s frustrating to have to navigate through multiple help files to pull together all the pieces you need. Roxygen2 provides several ways to avoid repeating yourself in code documentation, while assembling information from multiple places in one documentation file:

Cross-references

There are two tags that make it easier for people to navigate your documentation: @seealso and @family. @seealso allows you to point to other useful resources, either on the web <http://www.r-project.org> or to other documentation with [function_name()]. If you have a family of related functions, you can use @family {family} to cross-reference each function to every other function within the family. A function can be a member of multiple families.

For sum(), this might look like:

#' @family aggregations
#' @seealso [prod()] for products, [cumsum()] for cumulative sums, and
#'   [colSums()]/[rowSums()] marginal sums over high-dimensional arrays.

By default @family {family}, will generate the see also text “Other {family}:”, so the @family name should be plural (i.e., “model building helpers” not “model building helper”). You can override the default title by providing a rd_family_title list in man/roxygen/meta.R:

list(
  rd_family_title = list(aggregations = "Aggregation functions")
)

Inheriting documentation from other topics

You can inherit documentation from other functions in a few ways:

All of these work recursively so you can inherit documentation from a function that has inherited it from elsewhere.

You can also inherit documentation from functions provided by another package by using pkg::source_function.

Documenting multiple functions in the same file

You can document multiple functions in the same file by using either @rdname or @describeIn tag. It’s a technique best used with care: documenting too many functions in one place leads to confusion. Use it when all functions have the same (or very similar) arguments.

@describeIn

@describeIn is designed for the most common cases:

  • documenting methods in a generic
  • documenting methods in a class
  • documenting functions with the same (or similar arguments)

It generates a new section, named either “Methods (by class)”, “Methods (by generic)” or “Functions”. The section contains a bulleted list describing each function, labelled so that you know what function or method it’s talking about. Here’s an example documenting an imaginary new generic:

#' Foo bar generic
#'
#' @param x Object to foo.
foobar <- function(x) UseMethod("x")

#' @describeIn foobar Difference between the mean and the median
foobar.numeric <- function(x) abs(mean(x) - median(x))

#' @describeIn foobar First and last values pasted together in a string.
foobar.character <- function(x) paste0(x[1], "-", x[length(x)])

@rdname

@rdname is a more general-purpose tool. It overrides the default file name generated by roxygen and merges documentation for multiple objects into one file. This gives you complete freedom to combine documentation however you see fit. There are two ways to use @rdname. You can add documentation to an existing function:

#' Basic arithmetic
#'
#' @param x,y numeric vectors.
add <- function(x, y) x + y

#' @rdname add
times <- function(x, y) x * y

Or, you can create a dummy documentation file by documenting NULL and setting an informative @name.

#' Basic arithmetic
#'
#' @param x,y numeric vectors.
#' @name arith
NULL
#> NULL

#' @rdname arith
add <- function(x, y) x + y

#' @rdname arith
times <- function(x, y) x * y

Order of includes

By default, roxygen blocks are processed in the order in which they appear in the file. When you’re combining multiple files, this can sometimes cause the function usage to appear in a suboptimal order. You can override the default ordering with @order. For example, the following the block would place times first in arith.Rd because 1 comes before 2.

#' @rdname arith
#' @order 2
add <- function(x, y) x + y

#' @rdname arith
#' @order 1
times <- function(x, y) x * y

Evaluating arbitrary code

Another technique is the @eval tag. It evaluates code and treatments the result as if it was a literal roxygen tags. This makes it possible to eliminate duplication by writing functions. The code will be evaluated in the package environment and should yield a character vector of roxygen comments (but without the leading #').

For example, this code + roxygen block:

my_params <- function() {
  c(
    "@param x An integer vector",
    "@param y A character vector"
  )
}

#' A title
#' 
#' @eval my_params()
#' @export
foo <- function(x, y) {
}

Is equivalent to:

#' A title
#' 
#' @param x An integer vector
#' @param y A character vector
#' @export
foo <- function(x, y) {
}

Note that @eval cannot be embedded into another roxygen tag. If you want to dynamically generate part of a roxygen tag, see section ‘Dynamic R code’ in vignette("rd-formatting").

A related function is @evalRd. It works in the same way as @eval (i.e. it’s evaluated in the package environment) but rather than yielding roxygen comments that are processed as if they had been typed directly, it yields top-level Rd code that is inserted directly into the generated .Rd file. It is primarily useful if you want to generate Rd structure that is not currently supported by roxygen2.

For example, this block:

my_note <- function(x) {
  paste0("\\note{", paste0(x, "\n", collapse =""), "}")
}

#' @evalRd my_note(c(
#'   "This is the first line",
#'   "This is the second line"
#' ))
NULL
#> NULL

Would generate this Rd:

\note{
This is the first line
This is the second line
}

Roxygen templates

Roxygen templates are R files that contain only roxygen comments and that live in the man-roxygen directory. Use @template file-name (without extension) to insert the contents of a template into the current documentation.

You can make templates more flexible by using template variables defined with @templateVar name value. Template files are run with brew, so you can retrieve values (or execute any other arbitrary R code) with <%= name %>.

Note that templates are parsed a little differently to regular blocks, so you’ll need to explicitly set the title, description and details with @title, @description and @details.

Including external .Rmd/.md files

Starting from roxygen2 7.0.0, you can use @includeRmd path/to/file.Rmd to include an external .Rmd or .md document into a manual page (the path is relative from the source package root directory). You can include the same file in multiple documentation files, and for the first time, share content across documentation and vignettes.

Sections

@includeRmd supports headings in the external Rmd. The rules are as follows:

All content in the Rmd file will go either in the details or in new top level sections. It is currently not possible to document function arguments, return values, etc. in external Rmd documents.

Caching and figures

@includeRmd tries to set up knitr to support caching in the Rmd file. It sets the cache path to the default knitr cache path of the included Rmd file (i.e. foo/bar/file_cache/ for foo/bar/file.Rmd), so if you do not change the cache path within the Rmd itself, then everything should work out of the box. You should add these cache paths to .gitignore and .Rbuildignore.

@includeRmd also sets the knitr figure path of the (fig.path) to the default figure path of the included Rmd. Overriding this default is unlikely to work.

Sharing text between vignettes and the manual

@includeRmd helps avoiding repetition, as you can use the same .Rmd or .md document in the manual and also in the README.md file or in vignettes. One way to include an Rmd file in another one is to use child documents:

```{r child = "common.Rmd"}
```

If the Rmd file contains roxygen (Markdown-style) links to other help topics, then some care is needed, as those links will not work in Rmd files by default. A workaround is to specify external HTML links for them. These external locations will not be used for @includeRmd, which instead always links to the help topics in the manual. Example:

See also the [roxygen2::roxygenize()] function.

[roxygen2::roxygenize()]: https://roxygen2.r-lib.org/reference/roxygenize.html

This example will link to the supplied URLs in HTML / Markdown files and it will link to the roxygenize help topic in the manual.

Note that if you add external link targets like these, then roxygen will emit a warning about these link references being defined multiple times (once externally, and once to the help topic). This warning originates in Pandoc, and it is harmless.

Other tags

Indexing

Three other tags make it easier for the user to find documentation within R’s help system:

Apart from @keywords internal, these tags are not very useful because most people find documentation using Google. @keywords internal is useful because it removes the function from the documentation index; it’s useful for functions aimed primarily at other developers, not typical users of the package.

Back references

The original source location is added as a comment to the second line of each generated .Rd file in the following form:

% Please edit documentation in ...

roxygen2 tries to capture all locations from which the documentation is assembled. For code that generates R code with Roxygen comments (e.g., the Rcpp package), the @backref tag is provided. This allows specifying the “true” source of the documentation, and will substitute the default list of source files. Use one tag per source file:

#' @backref src/file.cpp
#' @backref src/file.h