SPECIES (version 1.2.0)

ChaoBunge: Coverage-duplication estimator for species richness

Description

This function calculates coverage-duplication based estimator from a Poisson-Gamma model by Chao and Bunge 2002.

Usage

ChaoBunge(n, t = 10,conf = 0.95)

Value

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

Nhat

point estimate.

SE

standard error(s) of the point estimate.

CI

confidence interval using a log transformation explained in Chao 1987.

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.

conf

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

Author

Ji-Ping Wang, Department of Statistics, Northwestern University

References

Chao, A. (1984), Nonparametric Estimation of the Number of Classes in a Population, Scandinavian Journal of Statistics, 11, 265-270.

Chao, A., and Bunge, J. (2002), Estimating the Number of Species in a Stochastic Abundance Model, Biometrics, 58, 531-539.

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
ChaoBunge(butterfly,t=10)