chao1: Chao1 Richness Estimator

In spacc: Fast Spatial Species Accumulation Curves

Chao1 Richness Estimator

Description

Estimate total species richness from abundance data using the Chao1 estimator (Chao 1984). Uses the number of singletons and doubletons to estimate undetected species.

Usage

chao1(x)

Arguments

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

Details

The Chao1 estimator is:

S_{Chao1} = S_{obs} + \frac{f_1^2}{2 f_2}

where f_1 is the number of singletons (species with total abundance 1) and f_2 is the number of doubletons (abundance 2).

When f_2 = 0, the bias-corrected form is used:

S_{Chao1} = S_{obs} + \frac{f_1 (f_1 - 1)}{2}

Value

An object of class spacc_estimate with components:

estimator

Name of the estimator ("chao1")

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 (singletons) and f2 (doubletons)

References

Chao, A. (1984). Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics, 11, 265-270.

Chao, A. (1987). Estimating the population size for capture-recapture data with unequal catchability. Biometrics, 43, 783-791.

See Also

chao2() for incidence-based estimation, ace() for abundance-based coverage estimator

Examples

species <- matrix(rpois(50 * 30, 2), nrow = 50)
chao1(species)

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