biocore/bipy — pull request #116 by jrrideout (2014-03-04 18:19:48+00:00)
Title: Add distance-based statistical methods

Adds two distance-based statistical methods (ANOSIM and PERMANOVA) in a new ```bipy.maths.stats.distance``` subpackage.

These methods were originally written in QIIME's ```qiime.stats``` module. I obtained permission from the original authors/contributors of this code to port the code here and change the license to BSD. The authors have been added to bipy's README.md.

The interface, design, and implementation are very different from the code in ```qiime.stats```. The code is also much faster: on a dataset that used to take a minute to process, both methods now only take ~2-3 seconds to run. The code is shorter, more numpythonic, and uses scipy (which wasn't a QIIME dependency when the code was originally written).

There are still more methods to port from QIIME, but I wanted to submit this pull request first for feedback. The docstrings are fairly minimal and I'd like to fill them out a bit more. However, I'm holding off for now to see what you guys think of the interface (borrows some ideas from ```bipy.maths.stats.ordination```).

Related to https://github.com/qiime/qiime/issues/1394.