phylo.beta.multi | R Documentation |
Computes 3 distance values accounting for the multiple-site phylogenetic turnover and nestedness components of phylogenetic beta diversity, and the sum of both values. Phylogenetic dissimilarities are based on Faith's phylogenetic diversity.
phylo.beta.multi(x, tree, index.family="sorensen")
x |
a community matrix or data frame, where rows are sites and columns are species. Alternatively |
tree |
a phylogenetic tree of class phylo with tips names identic to species names from the community matrix. |
index.family |
family of dissimilarity indices, partial match of |
The Sorensen dissimilarity index allows computing the PhyloSor index (Bryant et al. 2008) whereas the Jaccard dissimilarity index allows computing the UniFrac index (Lozupone & Knight 2005).
The function returns a list with three phylogenetic dissimilarity values.
For index.family="sorensen"
the three values are:
phylo.beta.sim |
|
phylo.beta.sne |
|
phylo.beta.sor |
|
For index.family="jaccard"
the three values are:
phylo.beta.jtu |
|
phylo.beta.jne |
|
phylo.beta.jac |
|
Julien De Bortoli (juldebortoli@yahoo.fr), Fabien Leprieur(fabien.leprieur@univ-montp2.fr), Andrés Baselga and David Orme
Baselga A. (2012) The relationship between species replacement, dissimilarity derived from nestedness, and nestedness. Global Ecology and Biogeography 21, 1223-1232
Bryant JA, Lamanna C, Morlon H, Kerkhoff AJ, Enquist BJ, et al. (2008) Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences of the United States of America 105: 11505-11511.
Faith DP, Lozupone CA, Nipperess D, Knight R (2009) The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology's "Phylogenetic Beta Diversity" Framework. Int J Mol Sci 10: 4723-4741. doi: 10.3390/ijms10114723.
Leprieur F, Albouy C, De Bortoli J, Cowman PF, Bellwood DR, et al. (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
Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71: 8228-8235.
phylo.betapart.core
, beta.multi
# toy tree for 6 species (sp1 to sp6)
require(ape)
toy.tree<-read.tree(text="(((sp1:1,sp2:1):5,(sp3:3,sp4:3):3):2,(sp5:7,sp6:7):1);")
plot(toy.tree)
# toy community table with 6 assemblages (A to F) with 6 species (sp1 to sp6)
toy.comm<-matrix(nrow=6, ncol=6)
rownames(toy.comm)<-c("A","B","C","D","E","F")
colnames(toy.comm)<-c("sp1","sp2","sp3","sp4","sp5","sp6")
toy.comm[1,]<-c(1,1,1,0,0,0)
toy.comm[2,]<-c(0,1,1,1,0,0)
toy.comm[3,]<-c(0,0,1,1,1,0)
toy.comm[4,]<-c(0,0,1,1,1,1)
toy.comm[5,]<-c(0,0,0,1,1,1)
toy.comm[6,]<-c(1,0,0,1,1,1)
toy.phylobetamulti<-phylo.beta.multi(toy.comm, toy.tree, index.family="sor")
toy.betamulti<-beta.multi(toy.comm, index.family="sor")
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