There are lots of different ways to create websites using R and R Markdown, with varying degrees of complexity and flexibility.
The easiest, most basic way to create a website is to knit a single Rmd file to a single HTML file. That’s what I’ve done in past GPL workshops, like here and here. Those are just single Rmd files that I knit to HTML and then put on a web server so that people can look at them.
Next you can create R Markdown websites (see full documentation here). This knits all the Rmd files in a folder and creates a menu so that they can tied together. I use these all the time for statistical analysis notebooks for each of my projects (like this and this). It’s also what I used for this website you’re looking at right now. It’s also what we’ll make together during the workshop.
Moving up the ladder of complexity, there’s Distill, which creates a complete website by knitting a folder full of Rmd files. It’s designed to be simple to use, so it has somewhat limited features, but you can still make full blown websites. I don’t use this, but lots of people do and these sites look neat.
The most complex and flexibly option is blogdown, which knits all the Rmd files in a folder and subfolders. This is what I use to build all my course websites and my personal website. It’s a little more complicated to use than Distill, but it gives you total control over every little aspect of the site and theme and template.