Thanks for the quick reply.
In this case, the raw data required to perform the tutorial analyses is way to big to embed in the package, so I have decided to leave these out (the published package does not include vignettes and builds fine). I am using pkgdown to create a website where all the documentation is hosted. I use pkgdown::build_site for this and it works great. I also build PDF versions from the same Rmd files and make them available on the site.
The problem is running build_site (which does a great job of pulling everything together) but still keeping the relative paths in the final published web pages. I could build each web page separately but that would be reinventing the (pkgdown) wheel. The PDFs are each built separately and are not part of this problem.
As I work through the problem more - it looks like the relative paths might not actually be the problem. I am getting an error from build_site.
Error : callr subprocess failed: pandoc document conversion failed with error 99
I cannot find any documentation on wht this error actually means - perhaps my assumption that it was linked to the file path issue I had is wrong...