phylosor: Phylogenetic index of beta-diversity PhyloSor
Description
Fraction of branch-length shared between two communities
Usage
phylosor(samp, tree)
Arguments
samp
Community data matrix
tree
Object of class phylo
Value
A distance object of the PhyloSor index of similarity between communities, the fraction of PD (branch-length) shared between two samples
Warning
The phylosor of all samples will include the branch length connecting taxa in those samples and the root of the supplied tree. The root of the supplied tree may not be spanned by any taxa in the sample. If you want the root of your tree to correspond to the most recent ancestor of the taxa actually present in your sample, you should prune the tree before running phylosor:
prunedTree <- prune.sample(sample,tree)
References
Bryant, J.B., Lamanna, C., Morlon, H., Kerkhoff, A.J., Enquist, B.J., Green, J.L. 2008. Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences 105 Supplement 1: 11505-11511