# R Documentation Patterns

> R documentation patterns with roxygen2, pkgdown, vignettes, examples, and package site structure.

- **Type:** Skill
- **Install:** `agentstack add skill-choxos-biostatagent-r-documentation-patterns`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [choxos](https://agentstack.voostack.com/s/choxos)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [choxos](https://github.com/choxos)
- **Source:** https://github.com/choxos/BiostatAgent/tree/main/plugins/r-tidy-modeling/skills/r-documentation-patterns

## Install

```sh
agentstack add skill-choxos-biostatagent-r-documentation-patterns
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# R Documentation Patterns

## Overview

Best practices and patterns for documenting R code, packages, and projects. Covers README files, code comments, function documentation, and project-level documentation.

## README Documentation

### README Structure

```markdown
# Package Name

[](https://github.com/user/pkg/actions/workflows/R-CMD-check.yaml)
[](https://CRAN.R-project.org/package=pkg)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://app.codecov.io/gh/user/pkg?branch=main)

## Overview

Brief description of what the package does (2-3 sentences).

## Installation

```r
# From CRAN
install.packages("pkg")

# Development version from GitHub
# install.packages("pak")
pak::pak("user/pkg")
```

## Usage

```r
library(pkg)

# Basic example
result 
  remove_missing() |>
  transform_variables()

# Analysis ----
# Fit statistical model

model = 4.1)
Imports:
    dplyr (>= 1.0.0),
    ggplot2
Suggests:
    testthat (>= 3.0.0),
    knitr,
    rmarkdown
VignetteBuilder: knitr
Config/testthat/edition: 3
```

### Package-Level Documentation

```r
#' pkgname: A package for doing something useful
#'
#' The pkgname package provides tools for X, Y, and Z.
#'
#' @section Main functions:
#' * [main_function()] - Does the main thing
#' * [helper_function()] - Helps with stuff
#'
#' @section Getting started:
#' See `vignette("pkgname")` for an introduction.
#'
#' @docType package
#' @name pkgname-package
#' @aliases pkgname
"_PACKAGE"
```

## Vignette Structure

### Basic Vignette

```r
---
title: "Getting Started with pkgname"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Getting Started with pkgname}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(pkgname)
```

## Introduction

Brief introduction to the package and its purpose.

## Installation

```{r, eval = FALSE}
install.packages("pkgname")
```

## Basic Usage

Walk through a simple example.

```{r}
# Example code
result  B[Input Validation]
    B --> C{Valid?}
    C -->|Yes| D[Data Processing]
    C -->|No| E[Error Message]
    D --> F[Model Fitting]
    F --> G[Results]
```

### Component Descriptions

```markdown
## Component Overview

### Data Layer
- `read_data()` - Import various data formats
- `validate_data()` - Check data integrity
- `transform_data()` - Prepare for analysis

### Analysis Layer
- `fit_model()` - Core model fitting
- `cross_validate()` - Performance assessment
- `tune_params()` - Hyperparameter optimization

### Output Layer
- `summarize_results()` - Generate summaries
- `export_results()` - Save to files
- `visualize_results()` - Create plots
```

## Dataset Documentation

```r
#' Example Patient Data
#'
#' A simulated dataset containing patient information for
#' demonstrating survival analysis methods.
#'
#' @format A data frame with 100 rows and 5 columns:
#' \describe{
#'   \item{patient_id}{Character. Unique patient identifier.}
#'   \item{age}{Numeric. Patient age in years.}
#'   \item{sex}{Factor with levels `"male"` and `"female"`.}
#'   \item{time}{Numeric. Follow-up time in days.}
#'   \item{status}{Integer. Event indicator (1 = event, 0 = censored).}
#' }
#'
#' @source Simulated data for illustration purposes.
#'
#' @examples
#' data(patients)
#' summary(patients)
"patients"
```

## Documentation Workflow

```r
# Generate documentation
devtools::document()

# Check documentation
devtools::check()

# Preview documentation
?function_name

# Build pkgdown site
pkgdown::build_site()
```

## Best Practices

1. **Be concise**: Documentation should be clear and to the point
2. **Use examples**: Include runnable examples for all exported functions
3. **Cross-reference**: Link to related functions and vignettes
4. **Keep updated**: Update docs when code changes
5. **Use markdown**: Enable markdown in roxygen2 for formatting
6. **Document edge cases**: Explain what happens with unusual inputs
7. **Include return values**: Always document what the function returns

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [choxos](https://github.com/choxos)
- **Source:** [choxos/BiostatAgent](https://github.com/choxos/BiostatAgent)
- **License:** MIT

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-choxos-biostatagent-r-documentation-patterns
- Seller: https://agentstack.voostack.com/s/choxos
- Browse the marketplace: https://agentstack.voostack.com/browse

---
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