R Documentation Generation

Generate comprehensive documentation from R codebases. This command uses the r-docs-architect agent to create roxygen2 documentation, README files, pkgdown sites, and architecture documentation.

Workflow Steps

1. Codebase Analysis

• Scan R files for functions and classes
• Identify exported vs internal functions
• Map function dependencies
• Detect existing documentation

2. Documentation Generation

Generate comprehensive documentation:

• roxygen2 function documentation
• Package-level documentation
• Dataset documentation
• Vignette outlines

3. README Creation

• Project overview
• Installation instructions
• Quick start examples
• Badge integration

4. pkgdown Configuration

• Site structure (_pkgdown.yml)
• Reference organization
• Article arrangement
• Custom styling

5. Architecture Documentation

• System diagrams (Mermaid)
• Component relationships
• Data flow visualization
• API reference

Usage

/r-doc-generate [path] [doc_type] [options]

Parameters

• path: Path to R package or project (default: current directory)
• doc_type: One of full, roxygen, readme, pkgdown, architecture (default: full)
• options: Comma-separated options (see below)

Documentation Types

full: Complete documentation suite

• All roxygen2 documentation
• README with badges
• pkgdown configuration
• Architecture diagrams
• Vignette templates

roxygen: Function documentation only

• roxygen2 comments for all functions
• Parameter documentation
• Return value documentation
• Examples

readme: README generation

• Project description
• Installation guide
• Usage examples
• Contributing guidelines

pkgdown: Website configuration

• _pkgdown.yml configuration
• Reference organization
• Article structure
• Theme settings

architecture: Architecture documentation

• System overview diagrams
• Component documentation
• Data flow diagrams
• API reference

Options

• overwrite: Overwrite existing docs (default: no)
• badges: Include badges in README (default: yes)
• examples: Generate examples (default: yes)
• vignettes: Create vignette templates (default: yes)

Output Location

output/
└── documentation/
    ├── man/                    # roxygen2 generated docs
    │   ├── function1.Rd
    │   └── function2.Rd
    ├── README.md               # Project README
    ├── _pkgdown.yml            # pkgdown configuration
    ├── vignettes/
    │   ├── getting-started.Rmd
    │   └── advanced-usage.Rmd
    └── architecture/
        ├── overview.md         # System overview
        └── diagrams/           # Mermaid/graphviz files

Example

/r-doc-generate my_package full badges,vignettes

This generates complete documentation for my_package with badges and vignettes.

Documentation Standards

roxygen2 Template

#' Function Title
#'
#' Detailed description of what the function does.
#'
#' @param x Description of parameter x.
#' @param y Description of parameter y.
#'
#' @return Description of return value.
#'
#' @examples
#' # Basic usage
#' result <- function_name(x = 1, y = 2)
#'
#' @export
#' @family related functions
#' @seealso [related_function()]

README Template

# Package Name

<!-- badges: start -->
[![R-CMD-check](badge-url)](badge-link)
[![CRAN status](badge-url)](badge-link)
<!-- badges: end -->

## Overview

Brief description of the package.

## Installation

```r
install.packages("pkg")

Usage

library(pkg)
# Basic example

Getting Help

• Documentation: https://user.github.io/pkg/
• Issues: https://github.com/user/pkg/issues

## Generated Content

### Function Documentation
- Auto-detects parameter types
- Generates @return based on function body analysis
- Creates runnable @examples
- Adds appropriate @export tags
- Links related functions with @family

### README Components
- Dynamic badges based on CI configuration
- Installation for CRAN and GitHub
- Usage examples from package functions
- Documentation links

### pkgdown Configuration
- Organizes functions by topic
- Groups related articles
- Configures search
- Sets up navigation

### Architecture Diagrams
- Function dependency graphs
- Data flow diagrams
- Package structure visualization
- API endpoint mapping

## Integration

### With devtools
```r
# After generating docs
devtools::document()
devtools::check()
pkgdown::build_site()

With GitHub Actions

Generated workflows include:

• Documentation building
• pkgdown deployment
• README rendering

Notes

• Original code is never modified
• All documentation goes to output/documentation/
• Review generated docs before integrating
• Templates follow tidyverse style