2. RMarkdown

RMarkdown is an authoring format that enables easy creation of dynamic documents, reports, and presentations. It combines text, written in easy-to-read-and-write markdown format, with embedded R code chunks. You can render the file to create an output document (in Word, PDF or HTML format) that includes the text, code, and results of the code (e.g. tables and visualizations).

I use this for two things:

  • In things like cleaning scripts, it allows me to combine the code, results and the documentation in one place. Raw code alone doesn’t mean much, especially if you can’t share the data along with it. A rendered RMarkdown data cleaning document contains the code, an explanataion of what the code does and why. This will include the tables and visualization such as boxplots, which go into deciding data cleaning actions. So even if you can’t share your data, you can share the rendered RMarkdown document, and it will still be useful for others to understand the logic behind your data cleaning decisions, and to adapt the code to their own data.
  • For outputs, such as reports and papers, it allows me to combine the code and writing in one place. This means I don’t have to copy and paste results into a word document every time I update my code. I just re-render the output document, and all results are updated.

How to get started with RMarkdown

This site will not go into the details of how to use RMarkdown, as there are many resources available online to get you started: