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Tech Check

• We suggest using the Chrome web browser.
• VERY Important!! If you haven’t already, please sign up for a free account at https://posit.cloud. We will use this as our platform today.
• Important! If you haven’t, please fill out the pre-course survey at https://redcap.link/pre_r_for_clinical_data.
• (optional) These slides are at https://joy-payton-chop.quarto.pub/intro-to-r-for-clinical-data-2023/
• (optional) The GitHub repo with exercises and solutions for this course as well as the slide deck source files in quarto is at https://github.com/arcus/intro-to-r-for-clinical-data

Introduction to R for Clinical Data

Presented by Arcus Education and the Children’s Hospital of Philadelphia (CHOP) R User Group

[Start at 0:02 past starting time.]

Hello and welcome to Introduction to R for Clinical Data, presented by the Children’s Hospital of Philadelphia (CHOP) R User Group and Arcus Data Education. We’re glad you’re here!

Introducing your Presenters and TAs!

Wes Wilson, Presenter

Stephan Kadauke, Presenter and Author

Rose Hartman, Presenter

We have several great Presenters and Teaching Assistants, including the folks whose names you see here. We don’t have time enough to go into the bios for all of our helpers here, but we want to thank all of them for their generosity of time. Presenters and TAs, please introduce yourself when we go into breakout sessions and when you start your presentations! We’ll start with our first three presenters: me (Wes), Stephan, and Kiley.

Introducing your Presenters and TAs!

Megha Lal, Presenter

Alexis Zavez, Teaching Assistant

Nick Brown, Teaching Assistant

Next, another speaker, Megha, and our first TAs, Alexis and Nick.

Our TA’s will be helping learners out one on one, so if you’re struggling, please reach out in chat and one of the TAs will help!

Introducing your Presenters and TAs!

Keith Baxelbaum, Teaching Assistant

Melissa Rosahl, Teaching Assistant

Rich Hanna, Teaching Assistant

Here’s three more TA’s: Keith, Mary Kate, and Rich.

Introducing your Presenters and TAs!

Kiley Yeaman, Teaching Assistant

Peace Maddox, TA

Joy Payton, Organizer / Tech

And finally, another pair of TAs, Kiley and Peace, and our Teams-ologist, Joy!

Familiarize yourself with:

• People
• Chat

The main part of the workshop will be webinar style, with everyone in one big session, and participants will be muted and cameras off. We are recording the main session for replay. One important thing we want to note is that in previous instances of this workshop, we used Zoom. This is our first time using Teams, so please be patient if things are a little clumsy sometimes. We’re unhappy with the data privacy policies at Zoom, so we’re going to give Teams a chance.

We will have one, possibly two breakout sessions. For the breakouts, we encourage you to participate by turning on your microphone. We also encourage you to turn on your camera, if you are comfortable, but that’s completely up to you. We won’t record breakout sessions.

This is the main Teams window. Across the top you should be able to see several buttons, including People and Chat.

Click on Chat to open the Chat window, and consider opening the People window, too. Opening the People window means you’ll see and place those windows somewhere you can see, if necessary by making your main Teams window a little smaller.

Non-Verbal Feedback

The “Thumbs up” or “Like” feedback with the check mark is important today!

We will make heavy use of the Non-verbal Feedback functionality of Teams At various points, we presenters will ask you to click “Thumbs Up” to let us know we can keep going. What I mean by that is to click the Thumbs Up icon in the “React” section at the top of the Teams window. Go ahead and find that “React” section of your screen now. We’ll ask you to use it in just a few moments.

Chat Window

Chat is the way we ask for help here.

The primary purpose of the Chat window, for this course, is to ask for help if you get stuck with a technical issue. If you don’t have a problem that someone is helping you with, you do not need to monitor the chat window to follow the course. I will also occasionally ask you to write the answer to a question in the chat.

Please note that when I’m presenting, I can’t also monitor the chat at the same time, so please don’t send me private messages. Instead, post to Everyone, briefly describing the problem you have, and you will get help by one of our TAs.

Your Turn #1

Click the “thumbs up” in the React menu. Then tell us where you work or what brought you here in the Chat window. If you haven’t already, also please create an account at https://posit.cloud, or be ready to create a project in your own RStudio from our GitHub repo

01:00

This brings us to the first interactive exercise! In the “React” section of Teams at the top of the screen, please click on the “thumbs up” button. When you do this, it tells us as presenters that you’re there, you’re listening, and you’re ready to continue.

Also, please tell us who you are! In the chat window, please tell us where you work or what brought you to this workshop. And if you haven’t already, please take this moment to sign up for a free account at https://posit.cloud.

We’ll give you about one minute to do this exercise.

Orientation to the Course

Great, now that we have technology squared away, let’s move ahead and learn about the scope of today’s learning.

The Data Analysis Pipeline

This workshop is a gentle introduction to data science designed for healthcare professionals and researchers who don’t have a background in programming. This slide shows a high-level conceptual framework of the most important steps of the data analysis process.

You always start by importing data and cleaning or “tidying” it up.

Then you start an iterative process of exploratory data analysis, which usually requires some data transformation.

The main engines of knowledge generation are visualization and modeling.

Finally, you need to communicate your results.

We will introduce the basics of all of these steps today, with the exception of modeling. Please note: there is more material in these slides than we have time in this workshop, but I wanted to leave all of this here for you to peruse on your own time. We will definitely be skipping some of the optional slides today.

Lecture Slides

In general, we will introduce new concepts with lecture slides like this one. We try to illustrate the concepts in a way that makes it easier to learn how to write code. Importantly, you will have access to the slides and be able to look at them again after you leave this course.

Timed Interactive Coding Exercises

After we present you with explanations, we’ll then practice these new skills with timed interactive coding exercises. For the coding exercises, we set up a training environment on the web specifically for this course.

Please note that these exercises are timed. It’s not essential that you finish each exercise, but it’s essential that you try. When the time is up, I ask that everyone stop working. After each coding exercise, we will come back together, and I will live code the exercise to catch everyone up.

Code of Conduct

https://https://github.com/arcus/intro-to-r-for-clinical-data/blob/main/conduct.md

One more serious thing I need to point out, since this is an interactive course - we want to provide a welcoming and supportive environment for all people, regardless of background or identity.

So we have a strict no-harassment policy: this includes abusive, offensive, or degrading language, in writing or in voice.

We also want people to feel that they can be themselves, especially in breakout rooms. While we will be recording this main session, we ask that participants refrain from taking screenshots or recording their fellow learners.

Your Turn #2

Meet and greet! We will send you into breakout rooms, where you will have a few minutes to meet one of our TAs and some of your fellow participants.

This brings us to our first breakout session! When the invitation appears to join a breakout room, please go ahead and join. We’d like you to share what brought you here and how you’re feeling about learning R – are you excited? Apprehensive? Confused?

For this exercise, we encourage you to turn on your microphone and camera, if you’re comfortable.

After about 10 minutes, we’ll bring everyone back into the main session. Depending on how many participants we have, there may be a lot of you in each break room, so we ask folks to be mindful of time when you introduce yourself and why you’re in this session.

Next Up: Introduction

Our next topic is:

Part 1: Introduction