recluster.dist: Compute a dissimilarity matrix using a battery of beta-diversity indices

Description

This function computes dissimilarity matrices based on the two most popular partitions of faunistic and phylogenitic beta-diversity. In particular Jaccard = beta3 + richness (Carvalho et al. 2012), Jaccard = Jturnover + Jnestedness (Baselga, 2012) and Sorensen = Simpson + nestedness (Baselga 2010) for faunistic indexes and Unifrac = Unifrac_turn + Unifrac_PD and PhyloSor = PhyloSor_turn + Phylosor_PD (Leprieur et al. 2012). Any other binary index can be included in brackets by using the syntax of designdist function of the vegan package.

Usage

recluster.dist(mat, phylo=NULL, dist="simpson")

Arguments

mat

A matrix containing sites (rows) and species (columns).

phylo

An ultrametric and rooted phylogenetic tree for species having the same labels as in mat columns. Only required for phylogenitic beta-diversity indexes.

dist

One among the 14 beta-diversity indexes

"simpson" "sorensen" "nestedness" "beta3" "richness" "jaccard" "jturnover" "jnestedness" "phylosor" "phylosort" "phylosorpd" "unifrac" "unifract" "unifracpd"

. Any custom binary dissimilarity can also be

Value

An object of class dist (see vegan:designdist for further details)

Details

Syntax for binary indices in vegdist: J, number of common species; A and B, number of species exclusive of the first and of the second site.

References

Baselga A. "Partitioning the turnover and nestedness components of beta diversity." Global Ecol Biogeogr (2010), 19: 134-143. Carvalho J. C., Cardoso P., Gomes P. "Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns." Global Ecol Biogeogr (2012), 21: 760-771. Leprieur F., Albouy C., De Bortoli J., Cowman P.F., Bellwood D.R., Mouillot D. "Quantifying Phylogenetic Beta Diversity: Distinguishing between 'True' Turnover of Lineages and Phylogenetic Diversity Gradients." Plos One (2012), 7 www.unifi.it/scibio/bioinfo/recluster.html