skbio.diversity.alpha.fisher_alpha¶
- skbio.diversity.alpha.fisher_alpha(counts)[source]¶
Calculate Fisher’s alpha, a metric of diversity.
State: Experimental as of 0.4.0.
Fisher’s alpha is estimated by solving the following equation for \(\alpha\):
\[S=\alpha\ln(1+\frac{N}{\alpha})\]where \(S\) is the number of OTUs and \(N\) is the total number of individuals in the sample.
- Parameters:
counts (1-D array_like, int) – Vector of counts.
- Returns:
Fisher’s alpha.
- Return type:
double
- Raises:
RuntimeError – If the optimizer fails to converge (error > 1.0).
Notes
The implementation here is based on the description given in the SDR-IV online manual [1]. Uses
scipy.optimize.minimize_scalar
to find Fisher’s alpha.References