ChaoShared: Estimation of the number of shared species in two communities
In JohnsonHsieh/ChaoShared: Statistical package 'ChaoShared'

Description Usage Arguments Value Author(s) References Examples

ChaoShared is a function to provide a shared species estimator in tow communities based on the following two sampling schemes.

In each community, a random sample of individuals is taken and species frequencies or abundances are recored;
Each communtiy is sample several times or the whole area is divided into several quadrats and species presence/absence data for multiple samples/quadrats are recorded.

1 2	ChaoShared(data, datatype = c("abundance", "incidence"), se = TRUE, nboot = 200, conf = 0.95)

`data`	a numerical matrix or a data frame with two columns. Each column represent the species abundances or incidence frequencies of each community. If `datatype = "incidence"`, then the input format of first entry should be total number of sampling units, and followed by species incidence frequencies in each column (See examples).
`datatype`	the data type of input data. That is individual-based abundance data (`datatype = "abundance"`) or presence/absence sample-base incidence data (`datatype = "incidence"`).
`se`	calculate bootstrap standard error and show confidence interval; default is `TRUE`.
`nboot`	the number of bootstrap resampling times, default is `200`.
`conf`	a positive number ≤ 1. "`conf`" specifies the confidence level for confidence interval. The default is `0.95`.

ChaoShared returns a list of two. First is the basic data informaiton; the other is a table of various estimators, their standard error and 100*conf % confidence interval.

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

Chao, A., Hwang, W.-H., Chen, Y.-C. and Kuo. C.-Y. (2000). Estimating the number of shared species in two communities. Statistica Sinica 10, 227-246.

Chao, A., Shen, T.-J. and Hwang, W. H. (2006). Application of Laplace's boundary-mode approximations to estimate species and shared species richness. Australian and New Zealand Journal of Statistics 48, 117-128.

Pan, H. Y., Chao, A. and Foissner, W. (2009). A non-parametric lower bound for the number of species shared by multiple communities. Journal of Agricultural, Biological and Environmental Statistics. 14, 452-468.

# load the individual-base (abundance) data
data(Birds2Estuaries)

# Estimation of shared species
ChaoShared(Birds2Estuaries, datatype="abundance", se=TRUE, nboot=200, conf=0.95)

# load the presence/absence sample-base (incidence) data
data(BBR)

# Estimation of shared species
ChaoShared(BBR, datatype="incidence", se=TRUE, nboot=200, conf=0.95)