beta.pair {betapart}R Documentation

Incidence-based pair-wise dissimilarities

Description

Computes 3 distance matrices accounting for the (i) turnover (replacement), (ii) nestedness-resultant component, and (iii) total dissimilarity (i.e. the sum of both components).

Usage

beta.pair(x, index.family = "sorensen")

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".

Value

The function returns a list with three dissimilarity matrices. For index.family="sorensen" the three matrices are:

beta.sim

dist object, dissimilarity matrix accounting for spatial turnover (replacement), measured as Simpson pair-wise dissimilarity

beta.sne

dist object, dissimilarity matrix accounting for nestedness-resultant dissimilarity, measured as the nestedness-fraction of Sorensen pair-wise dissimilarity

beta.sor

dist object, dissimilarity matrix accounting for total dissimilarity, measured as Sorensen pair-wise dissimilarity (a monotonic transformation of beta diversity)

For index.family="jaccard" the three matrices are:

beta.jtu

dist dissimilarity matrix accounting for spatial turnover, measured as the turnover-fraction of Jaccard pair-wise dissimilarity

beta.jne

dist object, dissimilarity matrix accounting for nestedness-resultant dissimilarity, measured as the nestedness-fraction of Jaccard pair-wise dissimilarity

beta.jac

dist object, dissimilarity matrix accounting for beta diversity, measured as Jaccard pair-wise dissimilarity (a monotonic transformation of beta diversity)

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.pair.abund, codebeta.multi, beta.sample, betapart.core, beta.temp

Examples

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

[Package betapart version 1.5.4 Index]