University of Utah

August 21-22, 2023

9:00 am - 5:00 pm MDT

Instructors: Rebecca Barter, George Vega Yon

Helpers: TBD

Registration

Register here
Cost: $100; payment can be coordinated through chart fields

Please note there is an opportunity for needs-based scholarships for this workshop. You can indicate your desire to be considered when registering for the workshop.

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. 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 "Best Practices for Scientific Computing".

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

Where: EHSEB Alumni Hall (8/21) and EHSEB 5100B (8/22), Salt Lake City, UT 84113. Get directions with OpenStreetMap or Google Maps.

When: August 21-22, 2023. Add to your Google Calendar.

Requirements: Participants should bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. Note: posit cloud access will be available for participants with installation issues. For instructions on installing R and RStudio, see the "Setup" section (below).

Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

Contact: Please email penny.atkins@hsc.utah.edu or rebecca.barter@hsc.utah.edu for more information.

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

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Collaborative Notes

We will use this etherpad (collaborative document) for chatting, taking notes, and sharing URLs and bits of code.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1

Before Pre-workshop survey
09:00 Introduction and setup
09:30 Introduction to RStudio and Quarto
10:15 Project management in RStudio
10:30 [Break]
10:45 Introduction to coding with R
12:00 [Lunch]
13:00 Vectors and types
14:30 [Break]
14:45 Subsetting vectors
15:15 Vectorization
16:00 END

Day 2

09:00 Intro to day 2
09:15 Subseting data frames
09:30 Data manipulation with dplyr
10:30 [Break]
10:45 Data manipulation with dplyr (continued)
12:00 [Lunch]
13:00 Data visualization with ggplot2
14:30 [Break]
14:45 Data visualization with ggplot2 (continued)
15:30 Post-workshop Survey
16:00 END

Setup

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

If installing R/RStudio locally, a list of common issues can be found on the Configuration Problems and Solutions wiki page.

We offer two setup routes for this workshop: (Option 1) Posit cloud and (Option 2) Using R/RStudio locally.

[Option 1 (recommended)] Posit Cloud

Posit cloud is a cloud-based resource that lets you use RStudio in your web browser, no local installation required. For this workshop, we have created a posit cloud instance that contains all of the workshop materials and data.

To get set up with posit cloud, you just need to create a free Posit cloud account and join the workshop's workspace.

[Option 2] Using R and RStudio "locally"

If you would prefer to use RStudio "locally" (i.e., use a version that you have installed on your computer), you will need to install R, RStudio, and Quarto (see instructions below), and you will need to download the workshop materials (quarto lesson files and datasets).

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

Note that even if you already have R and RStudio installed on your computer, we recommend updating them to the most recent version to ensure consistency with the workshop materials. To update your version of R and RStudio, you can follow the installation instructions below.

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

Instructions for R installation on various Linux platforms (debian, fedora, redhat, and ubuntu) can be found at <https://cran.r-project.org/bin/linux/>. These will instruct you to use your package manager (e.g. for Fedora run sudo dnf install R and for Debian/Ubuntu, add a ppa repository and then run sudo apt-get install r-base). Also, please install the RStudio IDE.

Quarto

Quarto is an open-source scientific and technical publishing system that lets us combine text, code, and outputs so that we can easily write reports and research papers. We create quarto documents within RStudio, but to use quarto, you need to install it from here.