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:
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
base : scalar, optional
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Returns: | double
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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 |