mcptools

mcptools implements the Model Context Protocol in R. There are two sides to mcptools:

R as an MCP server:

When configured with mcptools, MCP-enabled tools like Claude Desktop, Claude Code, and VS Code GitHub Copilot can run R code in the sessions you have running to answer your questions. While the package supports configuring arbitrary R functions, you may be interested in the btw package’s integrated support for mcptools, which provides a default set of tools to to peruse the documentation of packages you have installed, check out the objects in your global environment, and retrieve metadata about your session and platform.

R as an MCP client:

Register third-party MCP servers with ellmer chats to integrate additional context into e.g. shinychat and querychat apps.

Installation

Install mcptools from CRAN with:

install.packages("mcptools")

You can install the development version of mcptools like so:

pak::pak("posit-dev/mcptools")

R as an MCP server

mcptools can be hooked up to any application that supports MCP. For example, to use with Claude Desktop, you might paste the following in your Claude Desktop configuration (on macOS, at ~/Library/Application Support/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "r-mcptools": {
      "command": "Rscript",
      "args": ["-e", "mcptools::mcp_server()"]
    }
  }
}

Or, to use with Claude Code, you might type in a terminal:

claude mcp add -s "user" r-mcptools -- Rscript -e "mcptools::mcp_server()"

Then, if you’d like models to access variables in specific R sessions, call mcptools::mcp_session() in those sessions. (You might include a call to this function in your .Rprofile, perhaps using usethis::edit_r_profile(), to automatically register every session you start up.)

To deploy an HTTP MCP server to Posit Connect, add a _server.yml file with engine: mcptools and a tools file:

engine: mcptools
tools: tools.R

Deploy the directory as an R API and mark it as MCP content:

rsconnect::deployAPI(".", contentCategory = "mcp")

If the content URL is https://connect.example.com/content/abc123/, use https://connect.example.com/content/abc123/mcp as the MCP endpoint.

If you cannot set contentCategory = "mcp" during deployment, set the MCP category in Connect after deploying and set minimum processes to at least 1.

R as an MCP client

mcptools uses the Claude Desktop configuration file format to register third-party MCP servers, as most MCP servers provide setup instructions for Claude Desktop in their documentation. For example, here’s what the official GitHub MCP server configuration would look like:

{
  "mcpServers": {
    "github": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "-e",
        "GITHUB_PERSONAL_ACCESS_TOKEN",
        "ghcr.io/github/github-mcp-server"
      ],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "<YOUR_TOKEN>"
      }
    }
  }
}

Once the configuration file has been created (by default, mcptools will look to file.path("~", ".config", "mcptools", "config.json")), mcp_tools() will return a list of ellmer tools which you can pass directly to the $set_tools() method from ellmer:

ch <- ellmer::chat_anthropic()
ch$set_tools(mcp_tools())

ch$chat("What issues are open on posit-dev/mcptools?")

Example

In Claude Desktop, I’ll write the following:

“From what year is the earliest recorded sample in the forested data in my Positron session?”

Without mcptools, Claude couldn’t get far here; by default, it can’t run R code and doesn’t have any way to “speak to” my interactive R sessions.

Using the package, the model asks to describe the data frame using a structure that will show summary statistics from the data. mcptools will appropriately route the request to the open Positron session, forwarding the results back to the model for it to situate in a response.