iChao2: Improved Chao2 (iChao2) Richness Estimator

In spacc: Fast Spatial Species Accumulation Curves

Improved Chao2 (iChao2) Richness Estimator

Description

Estimate total species richness from incidence data using the improved Chao2 estimator (Chiu et al. 2014). Uses uniques through quadruplicates (Q1–Q4) to reduce bias for small samples.

Usage

iChao2(x)

Arguments

x	A site-by-species matrix (presence/absence or abundance). Automatically binarized.

Details

The improved Chao2 estimator is the incidence-based analogue of iChao1:

S_{iChao2} = S_{Chao2} + \frac{Q_3}{4 Q_4} \max\left(Q_1 - \frac{Q_2 Q_3}{2 Q_4}, 0\right)

When Q_4 = 0, the estimator collapses to Chao2.

Value

An object of class spacc_estimate with components:

estimator

Name of the estimator ("iChao2")

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 Q1, Q2, Q3, Q4, n_sites

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

chao2() for the standard estimator, iChao1() for abundance-based version

Examples

species <- matrix(rbinom(50 * 30, 1, 0.3), nrow = 50)
iChao2(species)

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