R for Reproducible Scientific Analysis

Institute for Modeling Collaboration and Innovation @ The University of Idaho

Nov 1 - Nov 3, 2022

Tues: 2-4:30 pm PT, Wed: 8 am-4 pm PT, Thur 2-4:30 pm

Instructors: James Van Leuven, Vicki Zhang, Max Czapanskiy, Bernard Ricca

Helpers: Pradeep Eranti, Breanna Sipley

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: Rm352 in the Integrated Research and Innovation Center (IRIC) building, University of Idaho, 875 Perimeter Dr., Moscow, ID. Get directions with OpenStreetMap or Google Maps.

When: Nov 1 - Nov 3, 2022. Add to your Google Calendar.

Requirements: Participants must bring a laptop 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 committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email jvanleuven@uidaho.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.


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

Pre-workshop Survey

Post-workshop Survey


Nov 1

Before Pre-workshop survey
02:00 Intro to R and RStudio
03:00 Break
03:10 Project Management
03:35 Getting Help
03:45 Data Structures

Nov 2

08:00 Data Structures
08:35 Data Frames
09:05 Break
09:10 Subsetting data
10:00 Control flow
10:45 Break
11:00 Control flow
11:15 Base graphics
11:30 Lunch
01:00 ggplot
02:15 Vectorization
02:35 Break
02:40 Functions
03:40 Writing Data
16:30 END

Nov 3

02:00 Review and questions
02:15 Data frame manipulation using dplyr
03:05 Break
03:10 Data frame manipulation using tidyr
04:00 Knitr??
16:30 Post-workshop Survey


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.

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

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, 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 (a terminal, RStudio, your web browser, etc..) and the window for the Zoom 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 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

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.

Please check the “Setup” page of the lesson site for instructions to follow to obtain the software and data you will need to follow the lesson.