R CMD Check gravy warning

[Namita Gupta]

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'gravy'
  ‘scale’
Documented arguments not in \usage in documentation object 'gravy':
  ‘aa’

Documented arguments not in \usage in documentation object 'rarefyDiversity':
  ‘min_c’

Undocumented arguments in documentation object 'regionProperties'
  ‘region_name’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

[Jason Vander Heiden]

I just fixed the 'min_c' one. The rest is man page cleanup in AnalyzeAa.R.

[Jason Vander Heiden]

Added missing @param directives in 7433a36 and b35e659.