At one point this worked. However, i left the project in what I thought was working condition and then come back to find that the formatting is all broken. The repo is available here and the site hosted here.
I've checked my _layouts/ folder and it has the / seemingly correctly set as per the answer here.
Similarly I've set my base URL as this is a project page as per this question.
Possibly something went wrong when I pushed the RMD file in, however I've tried to wind back and push that as the version of the repo, but I didn't see any changes (maybe I did this badly, I'm very new to github, and pretty novice at git).
How can I get my formatting back? The original structure was made using this tutorial on jekyll and ghpages.
FINAL SOLUTION:
After inspecting and testing both answers from LarsW and David_Jacquel, the final fix is as follows:
- _config.yml - include
baseurl: /Pokemon_FieldStudies - default.html - include
<link rel="stylesheet" type="text/css" href="{{ site.baseurl }}/css/main.css">
