write-roxygen-docs

name	write-roxygen-docs
description	Write roxygen2 documentation for R package functions, datasets, and classes. Covers all standard tags, cross-references, examples, and generating NAMESPACE entries. Follows tidyverse documentation style. Use when adding documentation to new exported functions, documenting internal helpers or datasets, documenting S3/S4/R6 classes and methods, or fixing documentation-related R CMD check notes.
license	MIT
allowed-tools	Read Write Edit Bash Grep Glob
metadata	{"author":"Philipp Thoss","version":"1.0","domain":"r-packages","complexity":"basic","language":"R","tags":"r, roxygen2, documentation, namespace"}

Write Roxygen Documentation

Create complete roxygen2 documentation for R package functions, datasets, and classes.

When to Use

• Adding documentation to a new exported function
• Documenting internal helper functions
• Documenting package datasets
• Documenting S3/S4/R6 classes and methods
• Fixing documentation-related R CMD check notes

Inputs

• Required: R function, dataset, or class to document
• Optional: Related functions for cross-referencing (@family, @seealso)
• Optional: Whether the function should be exported

Procedure

Step 1: Write Function Documentation

Place roxygen comments directly above the function:

#' Compute the weighted mean of a numeric vector
#'
#' Calculates the arithmetic mean of `x` weighted by `w`. Missing values
#' in either `x` or `w` are handled according to the `na.rm` parameter.
#'
#' @param x A numeric vector of values.
#' @param w A numeric vector of weights, same length as `x`.
#' @param na.rm Logical. Should missing values be removed? Default `FALSE`.
#'
#' @return A single numeric value representing the weighted mean.
#'
#' @examples
#' weighted_mean(1:5, rep(1, 5))
#' weighted_mean(c(1, 2, NA, 4), c(1, 1, 1, 1), na.rm = TRUE)
#'
#' @export
#' @family summary functions
#' @seealso [stats::weighted.mean()] for the base R equivalent
weighted_mean <- function(x, w, na.rm = FALSE) {
  # implementation
}

Expected: Complete roxygen block with title, description, @param for each parameter, @return, @examples, and @export.

On failure: If unsure about a tag, check ?roxygen2::rd_roclet. Common omission is @return, which is required by CRAN for all exported functions.

Step 2: Essential Tags Reference

Tag	Purpose	Required for export?
#' Title	First line, one sentence	Yes
#' Description	Paragraph after blank line	Yes
@param	Parameter documentation	Yes
@return	Return value description	Yes (CRAN)
@examples	Usage examples	Strongly recommended
@export	Add to NAMESPACE	Yes, for public API
@family	Group related functions	Recommended
@seealso	Cross-references	Optional
@keywords internal	Mark as internal	For non-exported docs

Expected: All required tags for the function type are identified. Exported functions have @param, @return, @examples, and @export at minimum.

On failure: If a tag is unfamiliar, consult the roxygen2 documentation for usage and syntax.

Step 3: Document Datasets

Create R/data.R:

#' Example dataset of city temperatures
#'
#' A dataset containing daily temperature readings for major cities.
#'
#' @format A data frame with 365 rows and 4 variables:
#' \describe{
#'   \item{date}{Date of observation}
#'   \item{city}{City name}
#'   \item{temp_c}{Temperature in Celsius}
#'   \item{humidity}{Relative humidity percentage}
#' }
#' @source \url{https://example.com/data}
"city_temperatures"

Expected: R/data.R contains roxygen blocks for each dataset with @format describing the structure and @source providing data provenance.

On failure: If R CMD check warns about undocumented datasets, ensure the quoted string (e.g., "city_temperatures") exactly matches the object name saved with usethis::use_data().

Step 4: Document the Package

Create R/packagename-package.R:

#' @keywords internal
"_PACKAGE"

## usethis namespace: start
## usethis namespace: end
NULL

Expected: R/packagename-package.R exists with @keywords internal and the "_PACKAGE" sentinel. Running devtools::document() generates man/packagename-package.Rd.

On failure: If R CMD check reports a missing package documentation page, verify the file is named R/<packagename>-package.R and contains the "_PACKAGE" string.

Step 5: Handle Special Cases

Functions with dots in names (S3 methods):

#' @export
#' @rdname process
process.myclass <- function(x, ...) {
  # S3 method
}

Reusing documentation with @inheritParams:

#' @inheritParams weighted_mean
#' @param trim Fraction of observations to trim.
trimmed_mean <- function(x, w, na.rm = FALSE, trim = 0.1) {
  # implementation
}

No visible binding fix using .data pronoun:

#' @importFrom rlang .data
my_function <- function(df) {
  dplyr::filter(df, .data$column > 5)
}

Expected: Special cases (S3 methods, inherited params, .data pronoun) are documented correctly. @rdname groups S3 methods together. @inheritParams reuses parameter docs without duplication.

On failure: If R CMD check warns about "no visible binding for global variable," add #' @importFrom rlang .data or use utils::globalVariables() as a last resort.

Step 6: Generate Documentation

devtools::document()

Expected: man/ directory updated with .Rd files for each documented object. NAMESPACE regenerated with correct exports and imports.

On failure: Check for roxygen syntax errors. Common issues: unclosed brackets in \describe{}, missing #' prefix on a line, or invalid tag names. Run devtools::document() again after fixing.

Validation

• Every exported function has @param, @return, and @examples
• devtools::document() runs without errors
• devtools::check() shows no documentation warnings
• @family tags group related functions correctly
• Examples run without errors (test with devtools::run_examples())

Common Pitfalls

• Missing @return: CRAN requires all exported functions to document their return value
• Examples that need internet/auth: Wrap in \dontrun{} with a comment explaining why
• Slow examples: Use \donttest{} for examples that work but take too long for CRAN
• Markdown in roxygen: Enable with Roxygen: list(markdown = TRUE) in DESCRIPTION
• Forgetting to run devtools::document(): Man pages are generated, not hand-written

Related Skills

• create-r-package - initial package setup including roxygen configuration
• write-testthat-tests - test the functions you document
• write-vignette - long-form documentation beyond function reference
• submit-to-cran - documentation requirements for CRAN