Quarto

In this two-day WGS course (formerly known as RMarkdown) you will be introduced to the basics of starting an R Project in Quarto: how to setup a decent file structure, how to import data and how to process them and how to export the results. Some example data will be used but it will also be possible to work on your own data. The course will have many practical assignments.

What is open science?

Open Science is the movement to make scientific research and data accessible to all. With Open Science decisions in experimental design, data collection, data processing, statistical analysis, and reporting should be transparent and reproducible for everybody. It is basically the old idea that scientific results should be reproducible by everyone and open to criticism.

What is the problem?

Many PhD students and other researchers use tools like Excel, SPSS or similar software to collect & store data from their experiments. They even use it for calculations and visualizations. Finally, results are transferred to Word for writing a paper and/or PowerPoint for creating a presentation. What is communicated to the outside world eventually as a final product in the form of a thesis, paper or presentation is hard to unravel for an outsider, let alone to reproduce it. In the process of transferring data, graphs, results of statistical analysis from one software program to another, it is not unlikely that errors will be made and some of them will go unnoticed (see, for instance, this Nature article: d41586-022-00563-z.pdf (nature.com)). The results have become irreproducible and the scientific path has become obscured (even for yourself and your team). Commercial software programs may not be accessible to everyone and therefore results may never be reproducible. This goes against the idea of open science.

RMarkdown

Quarto (previously RMarkdown) is a freely available software program that combines text, statistical analysis, and graphics into one file. Data storage, analysis, visualization and presentation of results (in a paper or presentation) takes places in a single file. This has the advantage that changes in a dataset are immediately processed in statistical models, graphs, reports and presentations. Workflows in Quarto can be considerably more efficient and therefore faster. Multiple Quarto files (e.g., each file being a paper) can easily be combined to form a thesis. Quarto documents can be converted into:

• Html pages
• Word files
• Pdf
• E-books
• Websites
• Presentation slides

Quarto can be combined with R, which runs on every computer platform. In practice, it is most convenient to use Quarto in combination with RStudio, also freely available. RStudio can be linked to version control systems like GIT and GITHub. In fact, you can use Quarto in RStudio just as a word processor without any knowledge of R but its strength is, of course, the combination of text with data processing, statistical analysis, graphing and reporting. Therefore, it only makes sense to participate in the course if you master R and RStudio to some extent (Python or Julia could also be used, but in the course it will be R).

In short, Quarto is yet another step forward in achieving Open Science, a tool every PhD student, postdoc and scientist should know about!

Former occurrences of this course

31 Oct – 3 Nov 2022   |   30-31 May 2022   |   6 and 13 Dec 2021   |   5-6 July 2021   |   21-22 Oct 2020