Removed R/ prefix from roxygenate dependencies

When Roxygenate runs collate to determine topological sort order of dependencies
It assumes that all files are in the R directory.

Explicitlly adding R/ prefixe in the @include statement throws an error
update_collate adds files R/* to Description
and then roxygenize tries to find them at R/R/*, which do not exist
Merge pull request #17 from johnmyleswhite/roxygen-dependencies

Removed R/ prefix from roxygenate dependencies, re-roxygenize with current roxygen2