About 30 minutes, once

Install CascadiaTools

A beginner's guide for Windows and Mac. If you have never used a terminal or Claude, start here.

Before you start

This takes about 30 minutes, once. Most of that time is waiting for downloads and installs. You do not need to know how to program. You will install three things:

  1. R, the free statistics program that runs the analyses on your computer;
  2. a compiler (Rtools on Windows, Apple's command-line tools on a Mac), which the Bayesian modules need to turn models into fast code;
  3. Claude Code, the AI assistant that talks to you and runs CascadiaTools.

Then you add CascadiaTools to Claude Code with two short commands, and ask Claude to finish the setup.

What you need

A Windows or Mac computer where you can install programs (on a university computer you may need IT to do it), an internet connection, and a Claude account with access to Claude Code (see Cost and accounts). Linux works too: install R and your distribution's build tools, then follow the same Claude steps.

Step by step

Choose your computer. The steps differ only for R and the compiler.

Windows

  1. Install R (version 4.5 or newer)

    Go to cran.r-project.org. Click Download R for Windows, then base, then the download link for the newest version. Open the file you downloaded and click through the installer, keeping the default options.

  2. Install Rtools (the compiler)

    Go to cran.r-project.org/bin/windows/Rtools and download the Rtools version that matches your R (for R 4.5, Rtools45). Run the installer with the default options.

    Rtools is needed for the Bayesian (Nimble) modules. Most other modules work without it, but install it now so nothing stops you later.

  3. Install Claude Code

    Go to claude.com/claude-code and download the Claude desktop app for Windows. Install it, open it and sign in with your Claude account. Then open the Code tab. (If you prefer a terminal, the terminal version of Claude Code works the same way; the same page explains how to install it.)

  4. Open a folder for your project

    Claude Code works inside one folder on your computer. Make a new, empty folder (for example my-first-analysis in your Documents) and choose it as the folder to work in.

  5. Add CascadiaTools

    Use whichever way suits you. Both install the same thing, and you only do this once.

    In the Claude desktop app (point and click)
    1. In the Code tab, open the plugins window: click the + button beside the message box and choose Add plugins, or type /plugin in the message box and press Enter.
    2. Go to Marketplaces, choose Add marketplace, enter taaltree/CascadiaTools and confirm. A marketplace called cascadia appears.
    3. Go to Discover (or Browse), find cascadia-tools and click Install. If it asks for a scope, choose User so CascadiaTools is available in all your projects.
    4. Close the window and start a new session (or type /reload-plugins) so Claude picks it up.

    Menu names can differ slightly between app versions; look for the plugins window, then a marketplace you can add by name.

    By typing two commands (desktop app or terminal)

    Type (or copy and paste) the first line into the message box and press Enter. When it finishes, do the same with the second line.

    /plugin marketplace add taaltree/CascadiaTools
    /plugin install cascadia-tools@cascadia

    The first line tells Claude Code where CascadiaTools lives; the second installs it. If typing /plugin opens the plugins window instead of running the line, finish with the point-and-click steps above. Afterwards, type /reload-plugins or start a new session.

  6. Finish setup: type “Set up CascadiaTools”

    Claude checks that R and the compiler work, installs the R packages the modules need (20 to 40 minutes the first time; you can keep working meanwhile), runs a short test, and asks whether your data are sensitive. It explains each step before doing it.

    When it says setup is complete, you are ready.

macOS

  1. Install R (version 4.5 or newer)

    Go to cran.r-project.org and click Download R for macOS. There are two installers: one for Apple silicon (M1, M2 and later chips) and one for older Intel Macs. To check which you have, open the Apple menu and choose About This Mac. Open the downloaded file and follow the installer.

  2. Install Apple's command-line tools (the compiler)

    Open the Terminal app (in Applications, then Utilities, or search for “Terminal” with Spotlight). Type this line and press Return:

    xcode-select --install

    A window asks whether to install the tools. Click Install and wait for it to finish. If it says the tools are already installed, you are done with this step. You can close Terminal afterwards; you won't need it again.

  3. Install Claude Code

    Go to claude.com/claude-code and download the Claude desktop app for macOS. Install it, open it and sign in with your Claude account. Then open the Code tab. (If you prefer a terminal, the terminal version of Claude Code works the same way; the same page explains how to install it.)

  4. Open a folder for your project

    Claude Code works inside one folder on your computer. Make a new, empty folder (for example my-first-analysis in your Documents) and choose it as the folder to work in.

  5. Add CascadiaTools

    Use whichever way suits you. Both install the same thing, and you only do this once.

    In the Claude desktop app (point and click)
    1. In the Code tab, open the plugins window: click the + button beside the message box and choose Add plugins, or type /plugin in the message box and press Enter.
    2. Go to Marketplaces, choose Add marketplace, enter taaltree/CascadiaTools and confirm. A marketplace called cascadia appears.
    3. Go to Discover (or Browse), find cascadia-tools and click Install. If it asks for a scope, choose User so CascadiaTools is available in all your projects.
    4. Close the window and start a new session (or type /reload-plugins) so Claude picks it up.

    Menu names can differ slightly between app versions; look for the plugins window, then a marketplace you can add by name.

    By typing two commands (desktop app or terminal)

    Type (or copy and paste) the first line into the message box and press Enter. When it finishes, do the same with the second line.

    /plugin marketplace add taaltree/CascadiaTools
    /plugin install cascadia-tools@cascadia

    The first line tells Claude Code where CascadiaTools lives; the second installs it. If typing /plugin opens the plugins window instead of running the line, finish with the point-and-click steps above. Afterwards, type /reload-plugins or start a new session.

  6. Finish setup: type “Set up CascadiaTools”

    Claude checks that R and the compiler work, installs the R packages the modules need (20 to 40 minutes the first time; you can keep working meanwhile), runs a short test, and asks whether your data are sensitive. It explains each step before doing it.

    When it says setup is complete, you are ready.

Your first analysis

When setup has finished, try one of these in Claude Code:

  • “Show me what CascadiaTools can do”
  • “Run the occupancy example”
  • or describe your own data and question. The finder gives you a prompt to start from.

A good habit: make one folder per project, put your original data files in a sub-folder called data_raw, and open the project folder in Claude Code. CascadiaTools never changes your original files.

Questions people ask

What is Claude Code?

Claude Code is an AI assistant made by Anthropic that works with the files in a folder on your computer. You type requests in your own words. It can read your data files, run programs such as R, and write results and reports into the folder. Before it runs a command or changes a file it may ask for your permission; read what it plans to do, then allow it.

CascadiaTools is a plugin for Claude Code: an add-on that gives Claude the validated analysis modules and the step-by-step checking rules described on this site.

What is a terminal, and do I need one?

A terminal is a window where you type commands instead of clicking. You mostly don't need one. The Claude desktop app has a Code tab with a normal chat box, and that is where you type everything on this page, including the two /plugin commands. On a Mac you open Terminal once, for the compiler. People who like terminals can use the terminal version of Claude Code instead; the commands are the same.

Cost and accounts

R, Rtools, Apple's command-line tools and CascadiaTools are free. Claude Code needs a Claude account with access to Claude Code, which usually means a paid plan. Plans and prices change, so check the current options at claude.com (your university may also have an agreement). Long Bayesian analyses can involve many messages with the agent, so heavier use can count more against plan limits.

Can I use it without AI?

Yes. The modules are ordinary R code with a command-line interface. Each module's worked example lists the commands. See the repository README and running without AI.

Troubleshooting

If something goes wrong, you can always describe the problem to Claude in your own words and paste the error message. These are the common ones.

“R not found”, or R is too old

Install R 4.5 or newer (step 1), then close and reopen the Claude app, open your project folder again and type “Set up CascadiaTools”. Programs started before R was installed can't see it.

If it still can't find R, tell Claude where R is installed. On Windows this is usually a folder like C:\Program Files\R\R-4.5.x; on a Mac, R is installed under /Library/Frameworks/R.framework.

Packages fail to install

The first setup installs many R packages and takes 20 to 40 minutes. If some fail, type “Set up CascadiaTools” again: setup checks what is missing and tells you which modules are affected. Common causes are a missing compiler (next item), no internet connection, or a university network that blocks downloads; ask your IT team about a proxy if downloads fail.

“Compiler not found”, or a Nimble model fails to build

The Bayesian modules use Nimble, which turns each model into C++ code and needs a compiler. On Windows install Rtools matching your R version; on a Mac run xcode-select --install in Terminal. Then restart Claude and run setup again. Modules that use maximum likelihood work without a compiler.

A Bayesian (Nimble) model is slow the first time

That is expected. Nimble compiles each model before it runs, which takes about 30 to 100 seconds, and then samples. Likelihood modules finish in minutes; Bayesian ones take longer. The planted-truth check fits 100 or more simulated data sets, so on a laptop it can take from minutes to hours depending on the module. The agent tells you what it is running.

Where are my results saved?

In your project folder, the one you opened in Claude Code. Reports (HTML), figures (PDF and PNG) and estimate tables go into a results folder there. Ask Claude “where is my report?” and it will tell you the exact file.

The /plugin commands are not recognised

Make sure you typed them in Claude Code (the desktop app's Code tab, or the terminal version), not in an ordinary Claude chat, and that each command is on its own line. Updating the Claude app to its newest version can help. You can also download the repository and add it from a folder: type /plugin marketplace add followed by the folder's path, then install as before.

CascadiaTools is made by Taal Levi, Cascadia Wildlife Lab, Oregon State University. Source code on GitHub · How to cite

Based at
Oregon State University