RMarkdown into Github Pages

Example of one of my Github pages:

You might have read this GitHub and RStudio tutorial by searching this topic. It is quite long and confusing as it tries to teach Git at the same time. You don’t need any of those branch operations. And the example yaml code is not indented correctly (corrected below).

Here is the short version:

1. Create in the root directory a yaml file: "_site.yml"

Make sure the yaml format is indented correct. Most errors come from a wrong format of the yml file, for example, I’d get an error “Format is not of class rmarkdown” when the rendering completes if I remove one space before theme: cosmo.

The following example as in the tutorial (format corrected) creates a navbar with website title “Cars”, home page named “HomePage” (using index.html) and another page called “Page 1” (using speed-and-distance.html).

The name of the html files href match your RMarkdown html output. I’d just name the .Rmd files with the same names

name: "cars"
output_dir: "docs"
navbar:
  title: "Cars"
  left:
    - text: "HomePage"
      href: index.html
    - text: "Page 1"
      href: speed-and-distance.html
output:
  html_document:
    theme: cosmo

How the navbar on the site looks like

Here is another example, the yaml file for the sample page posted in the beginning, you can check the repo to see how are the files organized.

name: "COVerAge_Plot"
output_dir: "docs"
navbar:
  title: "HOME"
  left: 
    - text: "Plots for COVerAGE-DB"
      href: index.html
    - text: "Country profile"
      href: country_report.html
output:
  html_document:
    theme: cosmo

2. Remove the knit and output part from the heading of .Rmd files So they don’t need their own output anymore

---
title: "Speed and Distance"
---

3. Render site

This will render every .Rmd file in the root directory.
Think the Github page as a one-page site with index.html as the homepage.

rmarkdown::render_site()

4. Push to Github

Make sure the homepage is named as index.html. Go to repo settings -> GitHub Pages and point the source to where thisindex.htmlfile is. Also you can change theme using the “Theme Chooser”.

You can only assign the short domain names like liuyanguu.github.io to one repo by changing the name of your repo into this URL (in my case, this blog, I have a repo named liuyanguu.github.io). All the rest pages and sites hosted on Github will have the repo name attached behind: liuyanguu.github.io/COVerAge_Plot (although this is not a page on this blog).