ChaoLee1992 {SPECIES}

Coverage-based estimators for species richness

Description

This function calculates ACE and ACE-1 estimators by Chao and Lee 1992 (ACE-1 provides further bias correction based on ACE).

Usage

       ChaoLee1992(n, t = 10, method = "all",conf = 0.95)

Arguments

n

a matrix or a numerical data frame of two columns. It is also called the “frequency of frequencies” data in literature. The first column is the frequency j=1, 2\ldots; and the second column is n_j, the number of species observed with j individuals in the sample.

t

a positive integer. t is the cutoff value to define the relatively less abundant species to be used in estimation. The frequencies n_j of j>t will not be used in estimating the sample coverage. The default value is t=10.

method

a string. It can be any one of “ACE”, “ACE-1”, or “all”. The default is “all”.

conf

a positive number \le 1. conf specifies the confidence level for confidence interval. The default is 0.95.

Value

The function ChaoLee1992 returns a list of: Nhat, SE and CI.

Nhat

point estimate of the specified method. If the default method=“all” is used, the function returns an estimate vector including ACE, ACE-1.

SE

standard error(s) of the point estimate(s).

CI

confidence interval using a log transformation explained in Chao 1987.

Author(s)

Ji-Ping Wang, Department of Statistics, Northwestern University

References

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

Chao, A., and Lee, S.-M. (1992), Estimating the Number of Classes via Sample Coverage, Journal of the American Statistical Association, 87, 210-217.

Examples

library(SPECIES)

##load data from the package, 
## "butterfly" is the famous butterfly data by Fisher 1943.

data(butterfly)

##output estimates from all 4 methods using cutoff t=10
ChaoLee1992(butterfly,t=10,method="all")

##output estimates from ACE method using cutoff t=10
ChaoLee1992(butterfly,t=10,method="ACE")