beta.sample: Resampling multiple-site dissimilarity for n sites

In betapart: Partitioning Beta Diversity into Turnover and Nestedness Components

Resampling multiple-site dissimilarity for n sites

Description

Resamples the 3 multiple-site dissimilarities (turnover, nestedness-resultant fraction, and overall beta diversity) for a subset of sites of the original data frame.

Usage

beta.sample(x, index.family="sorensen", sites=nrow(x$data), samples = 1)

Arguments

x	data frame, where rows are sites and columns are species. Alternatively x can be a betapart object derived from the betapart.core function.
index.family	family of dissimilarity indices, partial match of "sorensen" or "jaccard".
sites	number of sites for which multiple-site dissimilarities will be computed. If not specified, default is all sites.
samples	number of repetitions. If not specified, default is 1.

Value

The function returns a list with a dataframe with the resampled 3 multiple-site dissimilarities (turnover fraction, nestedness-resultant fraction and overall dissimilarity; see beta.multi), a vector with the respective means and a vector with the respective standard deviation.

For index.family="sorensen":

sampled.values	dataframe containing beta.SIM, beta.SNE and beta.SOR for all samples
mean.values	vector containing the mean values of beta.SIM, beta.SNE and beta.SOR among samples
sd.values	vector containing the sd values of beta.SIM, beta.SNE and beta.SOR among samples

For index.family="jaccard":

sampled.values	dataframe containing beta.JTU, beta.JNE and beta.JAC for all samples
mean.values	vector containing the mean values of beta.JTU, beta.JNE and beta.JAC among samples
sd.values	vector containing the sd values of beta.JTU, beta.JNE and beta.JAC among samples

Author(s)

Andrés Baselga and David Orme

References

Baselga, A. 2010. Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography 19:134-143

Baselga, A. 2012. The relationship between species replacement, dissimilarity derived from nestedness, and nestedness. Global Ecology and Biogeography 21, 1223-1232

See Also

beta.multi, beta.sample, beta.temp

Examples

# Read the data for Northern and Southern European cerambycids
data(ceram.s)
data(ceram.n)

# Resample 100 times the multiple-site dissimilarities
# for 10 countries.
beta.ceram.s<-beta.sample(ceram.s, index.family="sor", sites=10, samples=100)
beta.ceram.n<-beta.sample(ceram.n, index.family="sor", sites=10, samples=100)

# Plot the distributions of beta.SIM in Southern Europe (red) 
# and Northern Europe (blue)
plot(density(beta.ceram.s$sampled.values$beta.SIM), col="red", xlim=c(0,1))
lines(density(beta.ceram.n$sampled.values$beta.SIM), col="blue")

# Compute the p-value of difference in beta.SIM between South and North 
# (i.e. the probability of finding in the North a higher value than 
# in the South)
p.value.beta.SIM<-length(which(beta.ceram.s$sampled.values$beta.SIM<
beta.ceram.n$sampled.values$beta.SIM))/100

p.value.beta.SIM
# The result is 0 and we used 100 samples, so p<0.01

betapart documentation built on March 31, 2023, 10:29 p.m.