SpeciesIncidence: Estimation of Species richness for sample-based (incidence)...

In JohnsonHsieh/ChaoSpecies: Statistical package 'ChaoSpecies'

Description

SpeciesIncidence is a function to provide a Species richness estimator proposed by Chao (2005) et al.

There are seven other estimators which are Homogeneous Model(1994) estimators; Chao2 (1987) estimator; Chao2-bc (2005) estimator; ICE (1994) estimator; Ace-1 estimator; 1st order jackknife (1978) estimators and the 2nd order jackknife (1978) estimators.

Usage

SpeciesIncidence(data, method = c("all", "Homogeneous", "Chao", "CE", "Jackknife"),
                 k = 10, conf = 0.95)

Arguments

data	a vector of species incidence frequency and the input format of first entry should be total number of sampling units, and followed by species incidence frequency.
method	the method constructed to estimate entropy (see Details)
k	cut-off point. It is a value that separates frequency counts into abundant and rare groups
conf	a positive number ≤ 1. "conf" specifies the confidence level for confidence interval. The default is 0.95.

Details

• method = "all" : all estimators below involved. The default is "all"

• method = "Homogeneous" estimator, see Chao and Lee. (1992)

• method = "Chao" estimator, see Chao, Ann (1984 & 2005)

• method = "CE" estimator, see Chao and Lee. (1992)

• method = "Jackknife" estimator, see Burnham, K. P. and Overton, W. S. (1978)

Value

SpeciesIncidence returns a table of various species richness estimators, their standard error, 95 % confidence interval and CV_rare which the method you choose.

Author(s)

K.S. Tseng ; Y.H. Lee : Anne Chao
Maintainer : Anne Chao [e-mail]

References

Chao, A. and Lee, S.-M. (1992). Estimating the number of classes via sample converage. Journal of the American Statistical Association, 87, 210-217.

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

Chao, A. (2005). Species estimation and applications. Encyclopedia of Statistical Sciences, Second Edition, Vol. 12, 7907-7916 (N. Balakrishnan, C. B. Read and B. Vidakovic, Editors), Wiley, New York.

Burnham, K. P. and Overton, W. S. (1978). Estimaton of the size of a closed population when capture probabilities vary among naimals, Biometrika, 65, 625-633.

Examples

# load the sample-base (incidence) data
data(Ant_data)

# Estimation of species richness
SpeciesIncidence(Ant_data, method = "all", k=10, conf=0.95)

JohnsonHsieh/ChaoSpecies documentation built on May 7, 2019, 12:02 p.m.