skbio.diversity.alpha.simpson

skbio.diversity.alpha.simpson(counts)[source]

Calculate Simpson’s index.

State: Experimental as of 0.4.0.

Simpson’s index is defined as 1 - dominance:

\[1 - \sum{p_i^2}\]

where \(p_i\) is the proportion of the community represented by OTU \(i\).

Parameters

counts (1-D array_like, int) – Vector of counts.

Returns

Simpson’s index.

Return type

double

See also

dominance()

Notes

The implementation here is 1 - dominance as described in 1. Other references (such as 2) define Simpson’s index as 1 / dominance.

References

1

http://folk.uio.no/ohammer/past/diversity.html

2

http://www.pisces-conservation.com/sdrhelp/index.html