VUvAUMC Software Carpentry: R

Vrije Universiteit

Oct 06-10, 2025

10:00 - 15:00 CEST

Instructors: Bauke van der Velde, Elisa Rodenburg, Sophie Arnoult, Charlie Greene

Helpers: Anouk Vlug, Thomas Pronk, Sreenithya Avadakkam, Bauke van der Velde, Charlie Greene

General Information

The Carpentries project comprises the Software Carpentry, Data Carpentry, and Library Carpentry communities of Instructors, Trainers, Maintainers, helpers, and supporters who share a mission to teach foundational computational and data science skills to researchers.

Want to learn more and stay engaged with The Carpentries? Carpentries Clippings is The Carpentries' biweekly newsletter, where we share community news, community job postings, and more. Sign up to receive future editions and read our full archive: https://carpentries.org/newsletter/

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: 105 De Boelelaan. Get directions with OpenStreetMap or Google Maps.

When: Oct 06-10, 2025; 10:00 - 15:00 CEST 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. The workshop organizers have checked that:

The room is wheelchair / scooter accessible. Unfortunately the Tuesday afternoon and Wednesday are not accessible via wheelchair or scooter. if you use either of these please contact us and we will do our best to change the room or think with you to find a solution.
Accessible restrooms are available.

We are dedicated to providing a positive and accessible learning environment for all. We do not require participants to provide documentation of disabilities or disclose any unnecessary personal information. However, we do want to help create an inclusive, accessible experience for all participants. We encourage you to share any information that would be helpful to make your Carpentries experience accessible. To request an accommodation for this workshop, please fill out the accommodation request form. If you have questions or need assistance with the accommodation form please email us.

Glosario is a multilingual glossary for computing and data science terms. The glossary helps learners attend workshops and use our lessons to make sense of computational and programming jargon written in English by offering it in their native language. Translating data science terms also provides a teaching tool for Carpentries Instructors to reduce barriers for their learners.

Contact: Please email c.c.greene@vu.nl , b.vandervelde@amsterdamumc.nl , a.vlug@uva.nl or s.avadakkam@vu.nl 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 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 - Monday, 6th of October - HG-05A36 (Hoofdgebouw/Main building, 5th floor)

Before	Pre-workshop survey
10:00	Introduction to programming in R
11:20	Morning break
11:30	Introduction to programming in R (Continued)
12:30	Lunch break
13:15	Building Programs with R
14:00	Afternoon break
14:10	Building Programs with R (Continued)
14:45	Wrap-up
15:00	END

Day 2 - Tuesday, 7th of October - BV-0H36 (BelleVUe)

10:00	Making packages in R
11:20	Morning break
11:30	Data analysis with R
12:30	Lunch break
12:30	Room change to BV-1H26, up one floor.
13:15	Data analysis with R (Continued)
14:00	Afternoon break
14:10	Data analysis with R (Continued 2)
14:45	Wrap-up
15:00	END

Day 3 - Wednesday, 8th of October - BV-1H26 (BelleVUe)

10:00	Icebreaker
10:05	Files, folders, and paths in the unix shell
11:20	Morning break
11:30	Shell: Pipes and filters
12:30	Lunch break
13:15	Introduction to Git
14:00	Afternoon break
14:10	Introduction to Git (Continued 2)
14:45	Wrap-up
15:00	END

Day 4 - Friday, 10th of October - HG-05A36 (5th floor, main building

10:00	Git in action
11:20	Morning break
11:30	Git for collaboration
12:30	Lunch break
13:15	Open science in programming
14:00	Afternoon break
14:10	Question time: clarifying issues
14:45	Wrap-up
15:00	Post-workshop Survey
15:10	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.

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.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git can be downloaded from the git website where you can choose the installer that matches your needs. Most likely the x64 installer will be suitable for your machine and use. Allow it to make changes, and if needed right click on the installer exe file and choose 'run as admin'. In order to install you must allow it to make changes. Now follow the steps of the installer, if given the option install GitBash as well, it will be used in the shell part of the course.

Please open the Terminal app, type git --version and press Enter/Return. If it's not installed already, follow the instructions to Install the "command line developer tools". Do not click "Get Xcode", because that will take too long and is not necessary for our Git lesson. After installing these tools, there won't be anything in your /Applications folder, as they and Git are command line programs. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here. (Note: this project is no longer maintained.) Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open in the pop-up dialog.

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

R

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

Install R by:

Downloading and running this .exe file from CRAN.
Installing 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.

Install R by:

Downloading and running this .pkg file from CRAN.
Installing the RStudio IDE.

Install R by:

Navigating to CRAN and following the instructions outlined there, using your package manager. We have reproduced the commands below:

Use the terminal command prompt to type/copy-and-paste these commands in, pressing Enter after each line to run the command.
Do not run the lines with # at the start of each line, as this indicates a comment and is not part of the command.

    # update indices
    sudo apt update -qq

    # install two helper packages we need
    sudo apt install --no-install-recommends software-properties-common dirmngr

    # add the signing key for these repos
    wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

    # add the repo from CRAN
    sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

    # install R itself
    sudo apt install --no-install-recommends r-base

Installing the RStudio Server IDE:

    # install dependencies
    sudo apt install -y r-base-core r-recommended r-base-dev gdebi-core build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev
    sudo apt install --no-install-recommends gdebi-core

    # cd ~/Downloads

    # download the latest RStudio Server .deb file
    wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2025.05.1-513-amd64.deb

    # install the .deb file
    sudo gdebi rstudio-server-2025.05.1-513-amd64.deb

    # start the RStudio Server
    sudo systemctl start rstudio-server

    # enable RStudio Server to start on boot
    sudo systemctl enable rstudio-server

After installation of RStudio Server, check you can access it by:
- Opening a web browser and navigating to http://localhost:8787.
- Logging in with the username and password you used when you set up Linux / WSL2.

If you are using Windows and WSL2, the full in-depth instructions for installing R on WSL2 can be found in this POSIT article.