skbio.math.diversity.alpha.fisher_alpha

skbio.math.diversity.alpha.fisher_alpha(counts)[source]

Calculate Fisher’s alpha.

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 [R39]. Uses scipy.optimize.minimize_scalar to find Fisher’s alpha.

References

[R39](1, 2) http://www.pisces-conservation.com/sdrhelp/index.html