skbio.diversity.alpha.shannon#
- skbio.diversity.alpha.shannon(counts, base=2)[source]#
Calculate Shannon’s diversity index, default in bits.
Shannon’s diversity index, \(H'\), a.k.a., Shannon index, or Shannon- Wiener index, is defined as
\[H' = -\sum_{i=1}^s\left(p_i\log_2 p_i\right)\]where \(s\) is the number of taxa and \(p_i\) is the proportion of the sample represented by taxon \(i\).
- Parameters:
- counts1-D array_like, int
Vector of counts.
- basescalar, optional
Logarithm base to use in the calculation.
- Returns:
- double
Shannon’s diversity index.
Notes
Shannon’s diversity index was originally proposed in [1] as a measure of entropy.
The default logarithm base used here is 2 instead of \(e\).
References
[1]Shannon, C. E. (1948). A mathematical theory of communication. The Bell system technical journal, 27(3), 379-423.