part.p.tree {CommEcol}

Partition of pair-wise dissimilarity indices using phylogenetic/functional data

Description

This function computes the partition of pair-wise Sorensen and Jaccard dissimilarity indices described by Baselga (2011, 2012), but adapted for phylogenetic/functional data. The two resulting components are dissimilarities due to turnover and nestednes

Usage

part.p.tree(comm, tree, index.family = "sorensen")

Arguments

comm

Dataframe or matrix with samples in rows and species in columns.

tree

A phylogenetic/functional tree containing all species listed in comm.

index.family

The family of dissimilarity indices to be partitionated. Partial match to "sorensen" or "jaccard".

Value

A list including three dissimilarity matrices. The nomenclature of the matrices follows Baselga (2012). For the jaccard:

jac

Jaccard dissimilarity matrix.

jtu

The turnover component of the Jaccard index.

jne

The nestedness (or richness difference) component of the Jaccard index.

For the sorensen:

sor

Sorensen dissimilarity matrix.

sim

The turnover component of the Sorensen index (Simpson index).

sne

The nestedness (or richness difference) component of the Sorensen index.

Author(s)

Adriano Sanches Melo, with part of the code borrowed from phylosor (package picante).

References

Baselga, A. 2010. Partitioning the turnover and nestdness 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.

Leprieur, F., C. Albouy, J.D. Bortoli, P.F. Cowman, D.R. Bellwood and D. Mouillot. 2012. Quantifying phylogenetic beta diversity: distinguishing between 'true' turnover of lineages and phylogenetic diversity gradients. PLoS ONE 7(8), e42760. doi:10.1371/journal.pone.0042760

See Also

part.m.tree for multi-sample partitions.

Examples

library(picante)
data(sites4.6)
data(tree6)
part.p.tree(comm=sites4.6, tree=tree6, index.family="sorensen")