Intro to R Markdown templates

The basics

R Markdown

R Markdown is a simple markdown structure that allows you to combine text and code. A comprehensive introduction to R Markdown can be found here.

Parameterized R Markdown documemts

Parameterized R Markdown documents allow you to create reports with dynamic input. Parameters specified in the YAML header can be updated, producing a new report with new values and custom analysis.

This video gives an excellent introduction to parameterization in R Markdown.

Advanced R Markdown

The examples above are minimal examples. More complex reports can be created with more parameters and more rendering options. There are also additional technical tools that can be used to enhance R Markdown reports.

Bookdown

The bookdown package offers many useful extensions of the functionality of R Markdown. Most notably, documents created with bookdown are saved in a series of separate files (“chapters” or “sections”), allowing long reports to be broken up into more manageable chunks. Sections can easily be inserted and removed from the report.

Github Actions

Github Actions allow code to be run on a remote runner. When rendering a large number of reports, it can be time-consuming to render all of the reports on a local machine. With Github Actions, the reports can be rendered remotely and then deployed to a github pages website.