1.7.12 Formal Deprecation of Functions

Revise deprecated function documentation to match BioC standards
https://github.com/joey711/phyloseq/issues/269
1.7.12 Formal deprecation of outdated elements using .Deprecated
1.7.12 Formal Deprecation of Functions

	- Formal deprecation of functions using .Deprecated
		Issue 269,
		https://github.com/joey711/phyloseq/issues/269

	- Fixed bug in interface with vegan::fisher.alpha(..., se=TRUE).
		vegan doc states that this returns a data.frame,
		but a data.frame is not returned in vegan version 1.7.10.
		phyloseq no checks output dimensions before processing in
`estimate_richness`

	- Replaced deprecated functions in tests and documentation.
Merge branch 'Fix-Deprecated'