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 \(\alpha\):
where \(S\) is the number of OTUs and \(N\) is the total number of individuals in the sample.
counts (1-D array_like, int) – Vector of counts.
Fisher’s alpha.
double
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