ChaoSpecies: Estimation of Species richness

Description Usage Arguments Value Author(s) References See Also Examples

Description

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

For individual-based (abundance) data, there are eight estimators which are Homogeneous Model(1992) estimators; Homogeneous MLE (1992) estimator; Chao1 (1984) estimator; Chao1-bc (2005) estimator; ACE (1992) estimator; Ace-1 (1992) estimator; 1st order jackknife (1978) estimators and the 2nd order jackknife (1978) estimators.

For sample-based (incidence) data, 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

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ChaoSpecies(data, datatype = c("abundance", "incidence"), k = 10, conf = 0.95)

Arguments

data

a vector of species abundance or incidence frequency. If datatype = "incidence", then the input format of first entry should be total number of sampling units, and followed by species incidence frequency.

datatype

the data type of input data. That is individual-based abundance data (datatype = "abundance") or sample-based incidence data (datatype = "incidence").

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.

Value

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

Author(s)

K.S. Tseng ; Y.H. Lee : Anne Chao
Maintainer : Anne Chao chao@stat.nthu.edu.tw

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.

See Also

SpeciesAbundance, SpeciesIncidence

Examples

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# load the individual-base (abundance) data
data(Spider_data)

# Estimation of species richness
ChaoSpecies(Spider_data, datatype="abundance", k=10, conf=0.95)

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

# Estimation of species richness
ChaoSpecies(Ant_data, datatype="incidence", k=10, conf=0.95)

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