ChaoShared: Estimation of the number of shared species in two communities
In JohnsonHsieh/SpadeR: Species Prediction and Diversity Estimation with R

Description Usage Arguments Value Author(s) 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 confidence coefficient between 0 and 1.

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.

Anne Chao, K. H. Ma and T. C. Hsieh

# load the individual-base (abundance) data
data(SharedSpecDemoAbu)
# Estimation of shared species
ChaoShared(SharedSpecDemoAbu, datatype="abundance", se=TRUE, nboot=200, conf=0.95)
# load the presence/absence sample-base (incidence) data
data(SharedSpecDemoInci)
# Estimation of shared species
ChaoShared(SharedSpecDemoInci, datatype="incidence", se=TRUE, nboot=200, conf=0.95)