joey711/phyloseq — Issue #76: Central ecological distance wrapper
Author: joey711
Created: 2012-02-18 01:27:31+00:00
State: open
Labels: Feature

Should extend `vegdist`, `designdist`, `betadiver`, `dist`, `UniFrac` and `DPCoA` (when it exists) into one central `phyloseqDist` method that lays out options to calculate all these different distances from one central method.

Importantly, `designdist` also provides a way to define a custom distance calculation. Maintaining this functionality while also keeping a semantically streamlined interface may be challenging. A good option might be to separate the "canned" distances available in `designdist` from the custom part, and make custom distances a parameter option, with an optional distance definition that can be passed on to `designdist`.

The `phyloseq-class` handling will be easy, and collecting the parameters / documentation into one place will alone be a nice convenient resource for users.