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 bias-corrected version unless bias_corrected is
False
and there are both singletons and doubletons.- Parameters:
counts (1-D array_like, int) – Vector of counts.
bias_corrected (bool, optional) – Indicates whether or not to use the bias-corrected version of the equation. If
False
and there are both singletons and doubletons, the uncorrected version will be used. The biased-corrected 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 bias-corrected version is defined as
\[chao1=S_{obs}+\frac{F_1(F_1-1)}{2(F_2+1)}\]References