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

1

http://www.pisces-conservation.com/sdrhelp/index.html