Interface to the ITALIC Database of Lichen Biodiversity

A programmatic interface to the Web Service methods provided by ITALIC (< https://italic.units.it>). ITALIC is a database of lichen data in Italy and bordering European countries. 'ritalic' includes functions for retrieving information about lichen scientific names, geographic distribution, ecological data, morpho-functional traits and identification keys. More information about the data is available at < https://italic.units.it/?procedure=base&t=59&c=60>. The API documentation is available at < https://italic.units.it/?procedure=api>.

ritalic

ritalic is an R package which gives you access to ITALIC mediated data via its RESTful API.

ITALIC the Information System on Italian Lichens, makes available information and resources about the lichens known to occur in Italy and bordering countries. It is maintained and updated by the Research Unit of Professor Pier Luigi Nimis, at the University of Trieste (NE Italy), Department of Life Sciences. Most of the data are derived from the Checklist of the Lichens of Italy by Nimis (2016), but nomenclatural and distributional data are being continuously updated.

Installation

You can either install the stable relase of ritalic using the version available on CRAN:

# install ritalic
install.packages("ritalic")
# load ritalic
library(ritalic)

Or you can install the development version of the package from GitHub:

# install devtools package
install.packages("devtools")
# load devtools
library(devtools)
# install ritalic
devtools::install_github("plant-data/ritalic")
# load ritalic
library(ritalic)

# Now you can use the functions available in ritalic

Usage

Italic has a guide designed to help users: function and examples

Use ITALIC from AI assistants (MCP)

ritalic includes an MCP server, so that AI assistants (Claude, Positron Assistant, GitHub Copilot in VS Code, ...) can align names, retrieve the data of the taxa, search taxa by distribution, ecology and traits, and create identification keys, running the functions of ritalic on your computer.

Install the packages needed by the server:

install.packages(c("mcptools", "ellmer"))

Then add the server to the assistant. Claude Code:

claude mcp add ritalic -- Rscript -e "ritalic::italic_mcp_server()"

Claude Desktop, in claude_desktop_config.json:

{
  "mcpServers": {
    "ritalic": {
      "command": "Rscript",
      "args": ["-e", "ritalic::italic_mcp_server()"]
    }
  }
}

Positron (Posit Assistant), in ~/.posit/assistant/settings.json for all projects or .posit/assistant/settings.json for a single project:

{
  "mcpServers": {
    "ritalic": {
      "type": "local",
      "command": ["Rscript", "-e", "ritalic::italic_mcp_server()"],
      "timeout": 60000
    }
  }
}

The timeout (in milliseconds) gives R the time to start; type /mcp in the assistant to check that the server is connected.

VS Code (GitHub Copilot chat, agent mode), in .vscode/mcp.json for the workspace, or in the user configuration opened with the command MCP: Open User Configuration:

{
  "servers": {
    "ritalic": {
      "type": "stdio",
      "command": "Rscript",
      "args": ["-e", "ritalic::italic_mcp_server()"]
    }
  }
}

Start the server with the command MCP: List Servers (or the Start button shown above the server in mcp.json), then enable its tools in the tools picker of the chat.

Use the full path of Rscript if the assistant cannot find it (file.path(R.home("bin"), "Rscript") in R). The same tools can be used in an ellmer chat with chat$register_tools(italic_mcp_tools()).

Citation

Coming soon