Using RMarkdown and Jekyll together

2019-01-09 - This blog no longer uses Jekyll, and is built with the blogdown package and Hugo. It seemed useful to leave this up as a reminder, though.

I recently decided to rebuild this blog. I’ve scrapped the WordPress site (which I used before) and now the blog is built using Jekyll and RMarkdown. It’s hosted on GitHub here.

This will be a short post outlining how I did this, especially as making the switch seemed to me (at first) to be an overwhelming task. I’m assuming some (very) basic familiarity with both Git and Jekyll.

Step 1 - Prepare GitHub

The first thing you need is a GitHub repository ready for building a user website. I.e., GitHub Pages. The documentation for getting this set up is reasonably thorough, so I won’t go in to detail. In short, for a standalone website you need to:

  1. Create a repository named (so for me that’s

That’s pretty much it. Once this repository is in place you can point your browser at For me, this means that this blog can be found at (More on custom domains later).

Clone this (currently empty) repository to your local machine.

Step 2 - Install Jekyll

Again, the documentation for this is pretty good. I used the RubyGems method which seemed to work alright. I had some pain getting Ruby installed, but nothing that some Google-fu couldn’t solve. I should note that officially Jekyll requires Linux/macOS to work properly. Windows is only supported [unofficially](

Step 3 - Get knitr-jekyll

knitr-jekyll (from Yihui Xie) is how I was able to integrate RMarkdown/knitr with Jekyll to make blogging from R a little easier. You’ll also need the servr package (install.packages() in R will sort that out). You can find the knitr-jekyll repository here. Download the contents and save them into the local Git repository you made in step 1. Push the contents to GitHub and then direct yourself to your page ( You should see a page that looks like this.

Step 4 - Get a Jekyll theme

I’m using the mediator theme, but there are hundreds of themes available. Once you’ve chosen your theme, download it and copy it in to your local Git repository, overwriting the documents which are there already (the important R components from step 3 will remain). You should then be able to push straight to GitHub and view your new page. I say should as some themes will require a bit of extra work or have additional dependences. Most of those I looked at contained very helpful installation instructions.

Step 5 - Customise your site

You can now customise your site. Either by tweaking your theme to alter the appearance, changing/adding/remove settings in your Jekyll _config.yml files, or by building whole new layouts and pages into your theme using a combination of HTML, CSS/Sass, JavaScript and the Jekyll templating language, Liquid. Once you’re ready to build the site you can use servr::jekyll() (in the root directory of your blog) to build your site (and serve it locally) and push the results up to GitHub for display on your page.

Step 6 - Add content to your site

You are now in a position to start building your site. You can delete the default posts that came with knitr-jekyll/your theme and add your own. When using knitr-jekyll, posts written in RMarkdown should go in the _source folder. Upon running servr::jekyll(), your RMarkdown posts will be converted into Markdown and saved in to the _posts directory ready for upload to GitHub. Once you’re happy with the content, push the results to GitHub and check them out on your new page.

Step 5 - Get a custom domain (optional)

This foxed me for a while, but I found a very straightforward guide{:target="_blank"} which made things easy. If you’d like to use a custom domain name (for example I use thedatagent) for your new page, you’ll need to buy one from any popular domain registrar. Once you’ve done that you’ll need to set up a CNAME file in your Git repository: create a file called CNAME and add (in text) the custom domain you’ve bought inside it(e.g. my CNAME file simple contains Once you’ve done that, log in to your account on your domain registrar page and find the DNS Zone editor. You’ll need to add a new record to your DNS settings:

  1. Set the ‘host’ as www
  2. Enter CNAME as the type of DNS record to add
  3. Enter your GitHub user page (e.g. in the ‘Points to’ field
  4. Click add record

You will need to wait some time for these changes to propagate (I had to wait about 3 or 4), but once you’re done you should be up and running with your Jekyll-fuelled, RMarkdown-enabled, GitHub-hosted, custom-domain-name personal website.

Happy blogging!