By Cecilia Baldoni & Corné de Groot | May 25, 2025
The Member Engagement Committee runs Code Club every third Tuesday of the month. Time can vary depending on the host and will be announced at least two weeks in advance on SORTEE’s Slack. For more information, see SORTEE’s Code Club page.
On Tuesday, May 20th, we had an interactive Code Club session about using Quarto for writing manuscripts. Quarto is a code-based text editor, which provides an interface that integrates manuscript writing and analysis code, thereby improving reproducibility. Quarto is the next generation markdown format which has improved on several aspects of Rmarkdown. Quarto can be used in several other coding programmes like Rstudio, Python or Julia or a mix of different coding languages if they are installed. It can even be used to make presentation slides or write books!
This session was part 2 of a two-part series on Quarto, organised in collaboration with the SORTEE Outreach & Education team. The first instalment of this series was a webinar held on the 12th of May by Saoirse Kelleher. Saoirse gave a wonderful presentation about the background and basics of Quarto. This second instalment of the series involved a more informal and hands-on experience using Quarto within an Rstudio project.
We started by going through some of the markdown/Quarto basics together. An overview of these basics can be found on the Quarto webpage. Through an interactive exercise using Quarto syntax to introduce ourselves, we found out that some participants were familiar with Quarto and had used it before to write documents such as manuscripts, websites and theses. Next, we moved on to our example manuscript written in Quarto. Code for this example manuscript can be found on our GitHub page. We first discussed the YAML header (Yet Another Markdown Language), which is created for every new Quarto document. The YAML header is used to specify meta-data of the authors such as their affiliations and ORCID’s, and other specifications about the document, for instance the document type and citation style, making it very flexible for quick adjustments. We used the Palmer Penguin dataset (which is now embedded in base R) to create figures, and embedded that code and corresponding figures in the manuscript directly, highlighting the integration of code and manuscript as a great way to increase transparency! We then learnt to insert citations, figures and images in Quarto and how to format them. We hope that this demonstration, together with the Quarto webinar, inspires others to start writing in Quarto to improve upon reproducible workflows. Wewelcome any input, tips, and tricks anyone has discovered on their Quarto journey.
See you at the next Code Club session!
What’s next?
The next Code Club meeting will be on Tuesday, June 17th at 15:00-16:00h UTC +00:00** (the zoom link will be posted on SORTEE’s Slack). The next session will be a training session where we will give an Introduction to Shiny for building interactive webapps in R.
You can check the Code Club schedule here for upcoming meetings. To receive calendar invites in your local time zone, sign up here.
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To propose a Code Club meeting topic, please use this form.