biocore/scikit-bio — pull request #245 by ElBrogrammer (2014-04-02 20:42:13+00:00)
Title: DistanceMatrix -> DissimilarityMatrix, SymmetricDistanceMatrix -> DistanceMatrix

Fixes #242.

A couple of questions:

- Does anyone have the UniFrac Gain reference (preferably a paper, but a URL also works)? I mention this measure in a docstring, and it'd be nice to include a proper reference here.

- I'm on the fence about renaming the `skbio.core.distance` module to `skbio.core.dissimilarity`. Renaming it means that we'll be using a more general name for the module, which I like. However, `DistanceMatrix` will likely be the most-used thing from this module (most code uses this class because we require symmetry), and I'd like to push the use of `DistanceMatrix` over `DissimilarityMatrix` whenever possible because of the extra data validation it performs. For this reason, it might make sense to leave the module named `skbio.core.distance`. I don't have strong feelings about this- which module name makes the most sense?