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:

double

Simpson’s index.

See also

dominance

Notes

The implementation here is 1 - dominance as described in [R48]. Other references (such as [R49]) define Simpson’s index as 1 / dominance.

References

[R48](1, 2) http://folk.uio.no/ohammer/past/diversity.html
[R49](1, 2) http://www.pisces-conservation.com/sdrhelp/index.html