Welcome!

LLMs for Data Analysis in R

R/Medicine 2026

Welcome to LLMs for Data Analysis in R!

Workshop repo: https://github.com/skaltman/r-medicine-llm

☁️ Launch Instruqt environment:

1. Go to https://play.instruqt.com/posit/invite/18ocdvpujl2t
2. Click Start
3. It will take a few minutes to start up. When it’s ready, click the green Start button.
4. Click Open external Window
5. Open RStudio or Positron

About this workshop

👋 Introductions

🏡 skaltman.github.io/r-medicine-llm

All slides and info lives here!

You can follow along with the slides here has set up instructions but I’ll also give you some time in a minute

Workshop format

📊 Slides

💻 Demos

✏️ Exercises in Instruqt environment

Ask questions at any point in the chat

we’ll have lecture components with slides demos where I’ll show demo something and we’ll discuss how it works and interactive exercises where you’ll do some coding for these, I’ve set up a project for you in workbench via instruqt for you with everything you’ll need

if you have questions, you can put them in the chat at any time I can’t promise that I’ll see them while I’m talking, but during the exercise portions garrett and I will monitor it and also consolidate questions to answer when we regroup

Your Turn

Set up Instruqt:

1. Go to https://play.instruqt.com/posit/invite/omatxsihs3we
2. Click Start
3. It will take a few minutes to start up. When it’s ready, you’ll click the green Start button. (don’t worry if you don’t get to this)

01:00

ok so with that said we’re going to move into the first exericse which is just to start setting up your environment! it takes a few minutes to start up, so you’re going to start the process now, well talk for a bit, and then you’ll come back to it later and finish the process

Schedule

	Activity
👋	Intro
💬	LLM APIs from R
☕	Break
🛠️	Tool calling
🤖	Apps and coding agents
🌳	Privacy and security

here’s a rough schedule of what we’re going to be covering today this is only a three hour workshop, so there’s a lot more to discover afterwards

my goal is to show you what’s possible with llm apis from r and give you a good strating point so you’ll walk away understanding the basics of how to call llm apis from R, hook LLMs up to external tools, do some system prompt designing, make basic apps, and usign coding agents

File organization

_exercises/	Files for Your Turn exercises
_solutions/	Solutions to those exercises
_demos/	Files for demos

Let’s Dive In!

To use an LLM API…

…you (generally) need an API key!

we are going to be working with llm apis today and to use an api, you generally need an api key

How to get an API key, beyond this workshop

1. 🆙 Sign up for an account with OpenAI, Anthropic, etc.

2. 💳 Add a payment method

3. 🔑 Get an API key

4. 💾 Store it in .Renviron file
   as OPENAI_API_KEY, ANTHROPIC_API_KEY, etc.

(or your organization provides them to you)

this is likely what you’ll want to do if you want to run the exercises locally after this workshop is over

But we’ll give you API keys to use today!

1. Use these keys for all of our activities today

2. Explore! But please be considerate :)

3. We’ll turn them off at the end of the workshop

we will set this up next

Our Turn

Instruqt should now be ready to open.

1. Click the green Start button, then Open external window.
   
2. Click New Session and select either RStudio Pro or Positron Pro.
3. Click Launch.
4. Open the r-medicine-llm-exercises folder (do not create a project).

🔑 Set up keys:

1. Copy the code in the provided Google Doc.
2. Paste it into the R console and run.

🤖 Check that everything’s working:

• Run the code in _exercises/01_hello-llm/01_hello-llm.R

02:00

Send google doc in the chat!! we are going to do these steps together