Skip to contents

Estimate total species richness using the improved Chao1 estimator (Chiu et al. 2014). Uses singletons through quadrupletons (f1–f4) to reduce bias for small samples.

Usage

iChao1(x)

Arguments

x

A site-by-species matrix (abundance data). Columns are pooled across sites.

Value

An object of class spacc_estimate with components:

estimator

Name of the estimator ("iChao1")

estimate

Estimated total richness

se

Standard error of the estimate

lower

Lower 95 percent confidence bound

upper

Upper 95 percent confidence bound

S_obs

Observed species richness

details

List with f1, f2, f3, f4

Details

The improved Chao1 estimator adds a correction term using f3 and f4: $$S_{iChao1} = S_{Chao1} + \frac{f_3}{4 f_4} \max\left(f_1 - \frac{f_2 f_3}{2 f_4}, 0\right)$$

When \(f_4 = 0\), the estimator collapses to Chao1.

References

Chiu, C.H., Wang, Y.T., Walther, B.A. & Chao, A. (2014). An improved nonparametric lower bound of species richness via a modified Good-Turing frequency formula. Biometrics, 70, 671-682.

See also

chao1() for the standard estimator, iChao2() for incidence-based version

Examples

species <- matrix(rpois(50 * 30, 2), nrow = 50)
iChao1(species)