Created
May 7, 2014 09:26
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Simpson Diversity Index
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#!/usr/bin/env python | |
# Simpson Diversity Index | |
# http://en.wikipedia.org/wiki/Diversity_index | |
# modified from Shannon Diversity Index implementation by audy | |
# https://gist.github.com/audy/783125 | |
# https://gist.github.com/audy | |
def simpson_di(data): | |
""" Given a hash { 'species': count } , returns the Simpson Diversity Index | |
>>> simpson_di({'a': 10, 'b': 20, 'c': 30,}) | |
0.3888888888888889 | |
""" | |
def p(n, N): | |
""" Relative abundance """ | |
if n is 0: | |
return 0 | |
else: | |
return float(n)/N | |
N = sum(data.values()) | |
return sum(p(n, N)**2 for n in data.values() if n is not 0) | |
def inverse_simpson_di(data): | |
""" Given a hash { 'species': count } , returns the inverse Simpson Diversity Index | |
>>> inverse_simpson_di({'a': 10, 'b': 20, 'c': 30,}) | |
2.571428571428571 | |
""" | |
return float(1)/simpson_di(data) |
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