ChaoShared
: Estimation of shared species richness between two communities/assemblages based on
three types of data: Type (1) abundance data (datatype="abundance"), Type (2) incidencefrequency
data (datatype="incidence_freq"), and Type (2B) incidenceraw data (datatype="incidence
_raw"); see SpadeRpackage
details for data input formats.
1 2  ChaoShared(data, datatype = c("abundance", "incidence_freq", "incidence_raw"),
units, se = TRUE, nboot = 200, conf = 0.95)

data 
a matrix/data.frame of species abundances/incidences. 
datatype 
type of input data, "abundance", "incidence_freq" or "incidence_raw". 
units 
number of sampling units in each community. For 
se 
a logical variable to calculate the bootstrap standard error and the associated confidence interval. 
nboot 
an integer specifying the number of bootstrap replications. 
conf 
a positive number ≤ 1 specifying the level of confidence interval. 
a list of two objects:
$Basic_data_information
for summarizing data information.
$Estimation_results
for showing a table of various shared richess estimates, standard errors, and the associated confidence intervals.
Chao, A., Hwang, W.H., Chen, Y.C. and Kuo. C.Y. (2000). Estimating the number of shared species in two communities. Statistica Sinica, 10, 227246.
Pan, H.Y., Chao, A. and Foissner, W. (2009). A nonparametric lower bound for the number of species shared by multiple communities. Journal of Agricultural, Biological and Environmental Statistics, 14, 452468.
1 2 3 4 5 6 7  data(ChaoSharedData)
# Type (1) abundance data
ChaoShared(ChaoSharedData$Abu,"abundance",se=TRUE,nboot=200,conf=0.95)
# Type (2) incidencefrequency data
ChaoShared(ChaoSharedData$Inci,"incidence_freq",se=TRUE,nboot=200,conf=0.95)
# Type (2B) incidenceraw data
ChaoShared(ChaoSharedData$Inci_raw,"incidence_raw",units=c(16,17),se=TRUE,nboot=200,conf=0.95)

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