iChao1: Improved Chao1 (iChao1) Richness Estimator

In spacc: Fast Spatial Species Accumulation Curves

Improved Chao1 (iChao1) Richness Estimator

Description

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.

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.

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

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)

spacc documentation built on June 20, 2026, 5:07 p.m.