qiime/qiime — pull request #523 by wdwvt1 (2012-12-14 02:14:25+00:00)
Title: Alpha diversity changes

Many changes to resolve issue #103 and issue #255. Gini index has been implemented and added, Good's coverage has been implemented by @justin212k and I added it. Both additions were made in pycogent_backports/alpha_diversity.py which was added as well. qiime/conditional_uncovered_probability.py has been eliminated and all of its functions moved into the backport or into qiime/alpha_diversity.py. The script conditional_uncovered_probability.py has been left unchanged except that it can has known metrics 'robbins' or 'etsy_ci' as these seemed a better fit for the alpha_diversity.py script.
I have changed all files which referenced cogent.maths.stats.alpha_diversity (but made sure to look for anything that had cogent.maths.stats. as per @gregcaporaso's comment in issue #103) to reference qiime.pycogent_backports.alpha_diversity.
Test of the relevant files pass on my machine and the scripts are usable and calculate, though I didnt try every permutation of the options.