skbio.diversity.alpha.chao1¶

skbio.diversity.alpha.
chao1
(counts, bias_corrected=True)[source]¶ Calculate chao1 richness estimator.
State: Experimental as of 0.4.0.
Uses the biascorrected version unless bias_corrected is
False
and there are both singletons and doubletons. Parameters
counts (1D array_like, int) – Vector of counts.
bias_corrected (bool, optional) – Indicates whether or not to use the biascorrected version of the equation. If
False
and there are both singletons and doubletons, the uncorrected version will be used. The biasedcorrected version will be used otherwise.
 Returns
Computed chao1 richness estimator.
 Return type
double
See also
Notes
The uncorrected version is based on Equation 6 in 1:
\[chao1=S_{obs}+\frac{F_1^2}{2F_2}\]where \(F_1\) and \(F_2\) are the count of singletons and doubletons, respectively.
The biascorrected version is defined as
\[chao1=S_{obs}+\frac{F_1(F_11)}{2(F_2+1)}\]References
 1
Chao, A. 1984. Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 11, 265270.