I'm using rticles as a guide to create my own templates for use at our department. As per rticles, I added the .cls and .png file in the skeleton/ directory together with skeleton.Rmd. I also have a different directory resources, which contains the .tex read by pandoc. This is all exactly the same as rticles. In addition, the yaml file contains create_dir: true as required.
Problem: If I don't create an Rmd file using the template GUI (eg created as a standard html document and then switched the output to our own defined template), I can't build the PDF as pandoc complains it can't find the necessary cls files. Is there a way around this?