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.
Parameters: | counts (1-D array_like, int) – Vector of counts. |
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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 |