part.p.tree | R Documentation |
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
part.p.tree(comm, tree, index.family = "sorensen")
comm |
Dataframe or matrix with samples in rows and species in columns. |
tree |
A phylogenetic/functional tree containing all species listed in |
index.family |
The family of dissimilarity indices to be partitionated. Partial match to "sorensen" or "jaccard". |
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. |
Adriano Sanches Melo, with part of the code borrowed from phylosor
(package picante).
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
part.m.tree
for multi-sample partitions.
library(picante)
data(sites4.6)
data(tree6)
part.p.tree(comm=sites4.6, tree=tree6, index.family="sorensen")
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