SpeciesAbundance: Estimation of Species richness for individual- based...
In JohnsonHsieh/ChaoSpecies: Statistical package 'ChaoSpecies'

Description Usage Arguments Details Value Author(s) References Examples

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

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.

1 2	SpeciesAbundance(data, method = c("all", "Homogeneous", "Chao", "CE", "Jackknife"), k = 10, conf = 0.95)

`data`	a vector of species abundance 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`.

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)

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

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

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.

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

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