Working on our PH525x online course material, Rafa and I wanted to base all lecture material in Rmd files, as these are easy for students to load into RStudio to walk through the code. Additionally, the rendered markdown files can be displayed nicely on GitHub Pages (which uses Jekyll to turn markdown in HTML). All we needed to do is copy the markdown files into the /pages directory and they already look pretty great when viewed on github.com (also we borrowed the theme from Karl Broman’s simple site template). By adding MathJax to the header of the GitHub Page template, we also render latex math formula from the original Rmd files.
Below I go over the issues we encountered with including math, but you can jump to the bottom if you just want our solution.