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

chao1 confidence interval as (lower_bound, upper_bound).

Return type

tuple

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/