Second try for updating Roxygen code.

Along with the previously committed code, I added the Roxygen for the missing files. 

I'm not 100% sure how exactly the best way to document methods. Now that I'm looking at the built package with this code, I think there are some options for how best to document the methods. What I've committed does pass the CRAN check without warnings. I think if you don't want a separate line in the help pages list, you can remove the @aliases before each method, and it's still OK.  I could go either way as to what is better. 

Also worth noting, I didn't add any examples, so there are still some functions without working examples.