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:	double Fisher’s alpha.
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 [R5757]. Uses scipy.optimize.minimize_scalar to find Fisher’s alpha.

References

[R5757]

(1, 2) http://www.pisces-conservation.com/sdrhelp/index.html