As you may have learned already from relevant section in the Biology Procedures and Guidelines resource, R Markdown is a markup language that provides an easy way to produce a rich, fully-documented reproducible analysis. It allows its user to share a single file that contains all of the commentary, R code, and metadata needed to reproduce the analysis from beginning to end. R Markdown allows for “chunks” of R code to be included along with Markdown text to produce a nicely formatted HTML, PDF, or Word file without having to know any complicated programming languages or having to fuss with getting the formatting just right in a Microsoft Word DOCX file.
One R Markdown file can generate a variety of different formats and all of this is done in a single text file with a few bits of formatting. You’ll be pleasantly surprised at how easy it is to write an R Markdown document after your first few attempts.
We will be using R Markdown to create reproducible lab reports.
R Markdown is just one flavour of a markup language. RStudio can be used to edit R Markdown. There are many other markdown editors out there, but using RStudio is good for our purposes.