add R documentation back to github site under the manual tab

[warrenmcg]

@pimentel,

Here is the updated documentation. After reviewing how the site was set up and modified before to remove the R documentation, I followed your previous protocol instead of using the pkgdown package. I think the package will be a good idea moving forward for other packages, but it appears that the customization with the YAML file would require a lot more work to integrate with the existing site, and so this seemed to be the easiest option.

This doesn't update the site's changelog, vignettes, or other main pages that reference the version number or other information. It just updates the documentation that was in the manual page before.

[pimentel]

as usual, this looks great, @warrenmcg

thanks for doing this!