skbio.diversity.alpha.chao1_ci

skbio.diversity.alpha.chao1_ci(counts, bias_corrected=True, zscore=1.96)

Calculate chao1 confidence interval.

Parameters:

counts1-D array_like, int

Vector of counts.

bias_correctedbool, 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.

zscorescalar, optional

Score to use for confidence. Default of 1.96 is for a 95% confidence interval.

Returns:

tuple

chao1 confidence interval as (lower_bound, upper_bound).

See also

chao1

Notes

The implementation here is based on the equations in the EstimateS manual [1]. Different equations are employed to calculate the chao1 variance and confidence interval depending on bias_corrected and the presence/absence of singletons and/or doubletons.

Specifically, the following EstimateS equations are used:

1. No singletons, Equation 14.

2. Singletons but no doubletons, Equations 7, 13.

3. Singletons and doubletons, bias_corrected=True, Equations 6, 13.

4. Singletons and doubletons, bias_corrected=False, Equations 5, 13.

References

[1]

http://viceroy.eeb.uconn.edu/estimates/