ChaoShared: Estimation of the number of shared species between two...

In AnneChao/SpadeR: Species-Richness Prediction and Diversity Estimation with R

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 datatype = "incidence_raw", users must specify the number of sampling units taken from each community. This argument is not needed for "abundance" and "incidence_freq" data.
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.

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)

AnneChao/SpadeR documentation built on May 5, 2019, 6:03 a.m.