# Roxygen2 Pkgdown

> R package documentation with roxygen2 and pkgdown, including reference topics, articles, and site configuration.

- **Type:** Skill
- **Install:** `agentstack add skill-choxos-biostatagent-roxygen2-pkgdown`
- **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/roxygen2-pkgdown

## Install

```sh
agentstack add skill-choxos-biostatagent-roxygen2-pkgdown
```

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

## About

# roxygen2 and pkgdown

## Overview

Complete reference for roxygen2 documentation syntax and pkgdown site configuration. Covers all roxygen2 tags, cross-referencing, and advanced pkgdown customization.

## roxygen2 Fundamentals

### Basic Tags

```r
#' @title Short title (optional, first paragraph used if omitted)
#' @description Longer description (optional, second paragraph used if omitted)
#' @details Additional details section
#' @param name Description of parameter
#' @return Description of return value
#' @examples Runnable R code
#' @export Add function to NAMESPACE exports
#' @keywords keyword1 keyword2
#' @author Author Name
```

### Parameter Documentation

```r
#' @param x A numeric vector of values.
#' @param y Character string specifying the method. One of:
#'   - `"method1"`: Description of method 1
#'   - `"method2"`: Description of method 2
#' @param data A data frame containing:
#'   \describe{
#'     \item{col1}{Description of column 1}
#'     \item{col2}{Description of column 2}
#'   }
#' @param ... Additional arguments passed to [other_function()].
#' @param .data Internal use only. Data frame to process.
```

### Return Value Documentation

```r
#' @return A numeric vector of the same length as `x`.

#' @return A list with components:
#'   \describe{
#'     \item{fitted}{Fitted values from the model.}
#'     \item{residuals}{Model residuals.}
#'     \item{coefficients}{Named vector of coefficients.}
#'   }

#' @return A tibble with columns:
#'   * `term`: Character. The term name.
#'   * `estimate`: Numeric. Point estimate.
#'   * `std.error`: Numeric. Standard error.

#' @return Invisibly returns the input `x`.
```

### Examples

```r
#' @examples
#' # Basic usage
#' result = "4.0") export(new_function)
```

### S3 Methods

```r
#' @export
#' @method print myclass
print.myclass 
```

### Home Page Customization

```yaml
home:
  title: Package Name
  description: One-line description

  links:
    - text: Learn more
      href: https://example.com

  sidebar:
    structure: [links, license, community, citation, authors, dev]
```

### Articles Configuration

```yaml
articles:
  - title: Tutorials
    navbar: Tutorials
    contents:
      - articles/getting-started
      - articles/basic-usage

  - title: Advanced
    navbar: Advanced
    contents:
      - articles/advanced-topics

  - title: Internal
    contents:
      - articles/internal-docs
    # Not in navbar
```

## Building pkgdown Site

### Build Commands

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

# Build specific parts
pkgdown::build_home()
pkgdown::build_reference()
pkgdown::build_articles()
pkgdown::build_news()

# Preview locally
pkgdown::preview_site()

# Check site
pkgdown::check_pkgdown()
```

### GitHub Actions Deployment

```yaml
# .github/workflows/pkgdown.yaml
on:
  push:
    branches: [main, master]
  release:
    types: [published]
  workflow_dispatch:

name: pkgdown

jobs:
  pkgdown:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    permissions:
      contents: write
    steps:
      - uses: actions/checkout@v4
      - uses: r-lib/actions/setup-pandoc@v2
      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::pkgdown, local::.
          needs: website
      - name: Build site
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
        shell: Rscript {0}
      - name: Deploy to GitHub pages
        uses: JamesIves/github-pages-deploy-action@v4
        with:
          clean: false
          branch: gh-pages
          folder: docs
```

## Workflow

```r
# Development cycle
devtools::document()        # Generate man/ files
devtools::check()           # Check package
pkgdown::build_site()       # Build website

# Quick preview
pkgdown::build_reference_index()
pkgdown::build_article("vignette-name")
```

## Common Patterns

### Reexporting Functions

```r
#' @importFrom magrittr %>%
#' @export
magrittr::`%>%`

#' @importFrom rlang .data
#' @export
rlang::.data
```

### Deprecated Functions

```r
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' This function is deprecated. Use [new_function()] instead.
#'
#' @keywords internal
#' @export
old_function <- function(...) {
  lifecycle::deprecate_warn("1.0.0", "old_function()", "new_function()")
  new_function(...)
}
```

### Internal Functions

```r
#' Internal function
#'
#' @keywords internal
#' @noRd
internal_helper <- function(x) {}
```

## 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-roxygen2-pkgdown
- Seller: https://agentstack.voostack.com/s/choxos
- Browse the marketplace: https://agentstack.voostack.com/browse

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