skbio.diversity.alpha.shannon¶
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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