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

Shannon diversity index H.

Return type

double

Notes

The implementation here is based on the description given in the SDR-IV online manual 1 except that the default logarithm base used here is 2 instead of \(e\).

References

1

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