Introduction to R and RStudio

The Jackson Laboratory

Online

Tue & Thu, June 15-22

9am-12pm

Instructors: Sandeep Namburi, Sue McClatchy, Alexis Garretson, Samir Amin

Helpers: Ahmed Sadeque, George Savvidis, Olaitan Awe, Frank Zappulla, Maddie Gastonguay, Erick Ratamero, Naomie Gao

General Information

This course presents fundamental data skills needed to conduct research for researchers who have little to no prior computational experience. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at summer students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Tue & Thu, June 15-22. Add to your Google Calendar.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email susan.mcclatchy@jax.org or sandeep.namburi@jax.org for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.


Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code. You can also review the lesson material here.


Surveys

Please be sure to complete this survey after the workshop.

Post-workshop Survey


Schedule

Tue June 15

09:00 Introduction to R and RStudio
10:30 Morning break
11:00 Introduction to R and RStudio (Continued)
11:55 Wrap-up
12:00 END

Thu June 17

09:00 Loading and Exploring Data
10:30 Morning break
11:00 Transforming Data
11:55 Wrap-up
12:00 END

Tue June 22

09:00 Cleaning Data
10:30 Morning break
11:00 Data Visualization
11:50 Post-course survey & Wrap-up
12:00 END

Setup

To participate in a workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Install the videoconferencing client

Please download and install Webex to your computer.

Set up your workspace

You will be learning by "coding along" with the instructors. To do this, you will need to have both the window for the tool you will be learning about (RStudio, your web browser, etc..) and the window for the Webex video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

Video Tutorial

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.