Introduction

R Markdown documents can be used both to save and execute code and to generate reports in various formats. This is done by mixing markdown (as in the example above), and so-called code chunks in the same document. The code itself, as well as the output it generates, can be included in the final report.

R Markdown makes your analysis more reproducible by connecting your code, figures and descriptive text. You can use it to make reproducible reports, rather than e.g. copy-pasting figures into a Word document. You can also use it as a notebook, in the same way as lab notebooks are used in a wet lab setting (or as we utilise Jupyter notebooks in the tutorial after this one).

An example before we start? A screenshot of an R markdown file...

and on the right its result in HTML.