ChaoBunge: Coverage-duplication estimator for species richness

In SPECIES: Statistical Package for Species Richness Estimation

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)

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.

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.

Author(s)

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)

SPECIES documentation built on Aug. 21, 2023, 1:07 a.m.