Core calculations of betapart

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Description

Computes the basic quantities needed for computing the multiple-site beta diversity measures and pairwise dissimilarity matrices.

Usage

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Arguments

x

data frame, where rows are sites and columns are species

Value

The function returns an object of class betapart with the following elements:

sumSi

the sum of the species richness values of all sites

St

the total richness in the dataset

a

the multiple-site analog of the shared species term

shared

a matrix containing the number of species shared between pairs of sites

not.shared

a matrix containing the number of species not shared between pairs of sites: b, c

sum.not.shared

a matrix containing the total number of species not shared between pairs of sites: b+c

max.not.shared

a matrix containing the total maximum number of species not shared between pairs of sites: max(b,c)

min.not.shared

a matrix containing the total minimum number of species not shared between pairs of sites: min(b,c)

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.pair, beta.sample, beta.temp,

Examples

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data(ceram.s)
ceram.core.s<-betapart.core(ceram.s)
ceram.dist.jac<-beta.pair(ceram.core.s, index.family="jac")
ceram.dist.sor<-beta.pair(ceram.core.s, index.family="sor")
ceram.multi.jac<-beta.multi(ceram.core.s, index.family="jac")
ceram.multi.sor<-beta.multi(ceram.core.s, index.family="sor")