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.

Requirements: knowledge about R, e.g. the VLAG course “Introduction to R” by Jos Hageman or the PE&RC course “Ïntroduction to R and R Studio”.

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.

Quarto

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!

General Information

Target Group:	PhDs, postdocs
Group size:	max. 20 participants
Course duration:	2 days
Language:	English
Credit points:	0.6 ECTS
Self-study hours:
Name lecturer:	Jos Hageman (Biometris) and Tiny van Boekel (FQD)
Venue:	to be announced

 

Fee

Reduced fee: • PhD candidates of Wageningen University with an approved Training and Supervision Plan (TSP) who are registered at one of the WU graduate schools (EPS, PE&RC, VLAG, WASS, WIAS, WIMEK) • Postdocs of Wageningen University who are registered at one of the WU graduate schools	€ 160
University fee: All other PhD candidates / Wageningen University postdocs and staff	€ 320
External fee: All other participants	€ 640

Fee includes study and training material, coffee/tea and lunches.

Cancellation condition

You may cancel free of charge up to four weeks before the start of the course. After this date you will be charged the University fee. Unless:

• You can find someone to replace you in the course and supply the course coordinator with the name and contact information of your replacement.
  In this case you will only be charged a € 50 cancellation fee.
• You (PhDs and postdocs of Wageningen University) have a valid reason to cancel (illness or death in the family 1st or 2nd degree).
  In this case you will be charged the reduced fee and your supervisor/PI must send a mail indicating the reason for cancellation.

Information 

For more information please contact Suzanne van der Wielen (Suzanne.vanderwielen@wur.nl)