skbio.diversity.alpha.chao1_ci

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

Calculate chao1 confidence interval.

State: Experimental as of 0.4.0.

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.

zscore : scalar, 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 [R22]. 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

[R22](1, 2) http://viceroy.eeb.uconn.edu/estimates/