Outstanding `R CMD check` warnings

[Jason Vander Heiden]

This documentation exists. Not sure what the cause of the warning is:

* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘ChangeoClone’ ‘DiversityCurve’ ‘DiversityTest’
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

Just need to build vignettes before running check:

* checking package vignettes in ‘inst/doc’ ... WARNING
Package vignettes without corresponding PDF/HTML:
   ‘Diversity-Vignette.Rmd’
   ‘Lineage-Vignette.Rmd’

[Jason Vander Heiden]

Documenting S4 classes and methods:
https://github.com/variani/pckdev/wiki/Documenting-with-roxygen2

[Jason Vander Heiden]

Removed *.Rmd files from inst/doc

Updated class roxygen comments with:

#' @name         SomeClass-class
#' @rdname       SomeClass-class
#' @aliases      SomeClass
#' @exportClass  SomeClass