Tools for mixing code and output into formatted text documents have opened up multiple important possibilities for today’s scientists. Data cleaning, visualisation and analysis can now be incorporated into easily readable documents, allowing properly reproducible research alongside good, consistent and comprehensive records of analysis. Because the analysis and visualisation of data are part of the output document, when the data change it is straightforward to update the output document.

Rmarkdown is probably the best of these tools, allowing considerable customisation, high quality mathematical typesetting, the incorporation of R code not only as standalone “chunks” but also within otherwise standard text and a wide range of other features. Rmarkdown allows easy output to html, pdf and a variety of word processor formats as well as the production of pdf and html slides for presentations. When output to html it is easy to include interactive charts and tables and other forms of user interfaces that allow further interaction between the reader and the data.

This course is designed for academics and graduate students with an interest in reproducible research using Rmarkdown. We will cover all of the important techniques for generating elegant, reproducible documents in a wide variety of formats. A strong emphasis on hands-on exercises means that attendees will get ample opportunities to generate their own documents and gain experience of producing advanced and sophisticated documents using Rmarkdown.

No prior knowledge or experience with Rmarkdown is necessary. Some experience with R will be assumed but advanced R knowledge will not be necessary. Exercises will be designed to be run RStudio but users who wish to use other interfaces with R will also benefit.

• Understand the principles of literate programming and reproducible research

• Generating structured documents using markdown and incorporate R code into them

• Include material such as mathematical formulae, tables, footnotes and references

• Use chunk options to control the output of individual code chunks and global options and headers to customise the whole document

• Be able to proficiently generate documents in a variety of formats including html, pdf, MS word and html5 slides

• Customise documents using themes, html and LaTeX markup and include advanced html features such as tabs and interactive charts.

Monday - Classes from 9:30 to 17:30

Morning

- Introduction to reproducible research and literate programming
- What can I do with Rmarkdown?
- Markdown basics: document structure and text formatting

Registration deadline: 8th November 2019

Cancellation Policy:

> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.

Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.