part.m.tree {CommEcol}

Partition of multi-sample dissimilarity indices using phylogenetic/functional data

Description

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

Usage

part.m.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 the number of samples and three dissimilarity values. The nomenclature of the dissimilarities follows Baselga (2012). For the jaccard:

JAC

Multi-sample Jaccard dissimilarity index.

JTU

The turnover component of the Jaccard index.

JNE

The nestedness component of the Jaccard index.

For the sorensen:

SOR

Multi-sample Sorensen dissimilarity index.

SIM

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

SNE

The nestedness component of the Sorensen index.

Author(s)

Adriano Sanches Melo, but part of the code borrowed from beta.multi (package betapart) and 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.p.tree for pair-wise partitions.

Examples

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