RMarkdown

In the two day WGS course you will be introduced to the basics of starting an R Project in RMarkdown: 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 or SPSS 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 eventually communicated to the outside world 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. 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

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

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

The core of RMarkdown is the freely available software program R that runs on every computer platform. In practice, it is most convenient to use RStudio, also freely available. RStudio can be linked to version control systems like GIT and GITHub. In fact, you can use RMarkdown 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, so in practice it only makes sense if you master R to some extent.

Former occurrences of this course

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