ChaoShared {SpadeR} | R Documentation |
Estimation of the number of shared species between two communities/assemblages
Description
ChaoShared
: Estimation of shared species richness between two communities/assemblages based on
three types of data: Type (1) abundance data (datatype="abundance"), Type (2) incidence-frequency
data (datatype="incidence_freq"), and Type (2B) incidence-raw data (datatype="incidence
_raw"); see SpadeR-package
details for data input formats.
Usage
ChaoShared(data, datatype = c("abundance", "incidence_freq", "incidence_raw"),
units, se = TRUE, nboot = 200, conf = 0.95)
Arguments
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 |
Value
a list of two objects:
$Basic_data_information
for summarizing data information.
$Estimation_results
for showing a table of various shared richess estimates, standard errors, and the associated confidence intervals.
References
Chao, A., Hwang, W.-H., Chen, Y.-C. and Kuo. C.-Y. (2000). Estimating the number of shared species in two communities. Statistica Sinica, 10, 227-246.
Pan, H.-Y., Chao, A. and Foissner, W. (2009). A non-parametric lower bound for the number of species shared by multiple communities. Journal of Agricultural, Biological and Environmental Statistics, 14, 452-468.
Examples
data(ChaoSharedData)
# Type (1) abundance data
ChaoShared(ChaoSharedData$Abu,"abundance",se=TRUE,nboot=200,conf=0.95)
# Type (2) incidence-frequency data
ChaoShared(ChaoSharedData$Inci,"incidence_freq",se=TRUE,nboot=200,conf=0.95)
# Type (2B) incidence-raw data
ChaoShared(ChaoSharedData$Inci_raw,"incidence_raw",units=c(16,17),se=TRUE,nboot=200,conf=0.95)