MCP Setup

AI Agent Integration Guide

This guide covers how to integrate MCPR with different AI coding assistants.

Supported Agents

MCPR currently supports: - Claude Desktop - Gemini (via MCP) - GitHub Copilot (via MCP)

Claude Desktop Setup

Automatic Configuration

library(MCPR)
install_mcpr(agent = "claude")

Manual Configuration

Edit your Claude Desktop config file:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json Windows: %APPDATA%\Claude\claude_desktop_config.json
Linux: ~/.config/claude/claude_desktop_config.json

Add the MCP server configuration:

{
  "mcpServers": {
    "mcpr": {
      "command": "R",
      "args": ["--quiet", "--slave", "-e", "MCPR::mcpr_server()"]
    }
  }
}

Using MCPR Tools

Once configured, your AI agent will have access to these tools:

Session Management

• manage_r_sessions('list') - List active R sessions
• manage_r_sessions('join', session=ID) - Connect to a session
• manage_r_sessions('start') - Start a new session

Code Execution

• execute_r_code(code) - Run R code in the connected session

Visualization

• create_plot(expr, width, height, format) - Generate plots

Inspection

• view('session') - View workspace objects
• view('terminal') - View command history
  
• view('workspace') - View file system context

Workflow Examples

Data Analysis Workflow

1. Start R session: mcpr_session_start()
2. Agent joins session: manage_r_sessions('join', session=1)
3. Load data: execute_r_code("data <- read.csv('data.csv')")
4. Explore: view('session') to see loaded objects
5. Visualize: create_plot("plot(data$x, data$y)")
6. Iterate and refine analysis

Multi-Session Development

• Session 1: Data preprocessing
• Session 2: Model development
  
• Session 3: Visualization and reporting

Troubleshooting

Agent can’t see tools: Restart the agent after configuration.

Permission errors: Check file paths and R library permissions.

Connection timeouts: Increase timeout in MCP configuration.

Advanced Configuration

Custom Tool Paths

{
  "mcpServers": {
    "mcpr": {
      "command": "R",
      "args": ["--quiet", "--slave", "-e", "MCPR::mcpr_server()"],
      "env": {
        "MCPTOOLS_TOOLS_DIR": "/path/to/custom/tools",
        "MCPTOOLS_LOG_FILE": "/path/to/logs/mcpr.log"
      }
    }
  }
}

Environment Variables

• MCPTOOLS_LOG_FILE: Path for debug logs
• MCPTOOLS_TOOLS_DIR: Custom tools directory
• R_LIBS_USER: R library path