Description Usage Arguments Value Author(s) References See Also Examples
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.
1 | ChaoSpecies(data, datatype = c("abundance", "incidence"), k = 10, conf = 0.95)
|
data |
a vector of species abundance or incidence frequency. If |
datatype |
the data type of input data. That is individual-based abundance data ( |
k |
cut-off point. It is a value that separates frequency counts into abundant and rare groups |
conf |
a positive number ≤ 1. " |
ChaoSpecies returns a table of various species 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.
SpeciesAbundance
,
SpeciesIncidence
1 2 3 4 5 6 7 8 9 10 11 | # 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)
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