skbio.diversity.alpha.shannon

skbio.diversity.alpha.shannon(counts, base=2)[source]

Calculate Shannon entropy of counts, default in bits.

State: Experimental as of 0.4.0.

Shannon-Wiener diversity index is defined as:

\[H = -\sum_{i=1}^s\left(p_i\log_2 p_i\right)\]

where \(s\) is the number of OTUs and \(p_i\) is the proportion of the community represented by OTU \(i\).

Parameters:

counts : 1-D array_like, int

Vector of counts.

base : scalar, optional

Logarithm base to use in the calculations.

Returns:

double

Shannon diversity index H.

Notes

The implementation here is based on the description given in the SDR-IV online manual [R47] except that the default logarithm base used here is 2 instead of \(e\).

References

[R47](1, 2) http://www.pisces-conservation.com/sdrhelp/index.html