phylotools (version 0.1.2)

phylocom.phylosor: Calculating Phylosor similarity

Description

This function can be used to calculating phylosor (Phylogenetic Sorenson ) similarity between each pair of places

Usage

phylocom.phylosor(sample.file = "sample", phylo = "phylo")

Arguments

sample.file

Phylocom "Sample" file in the working directory .

phylo

The phylo file in the working directory, must be in newick format.

Value

a distance matrix

Details

This function has been tested for calculating phylosor for very large phylogenies (more than 17000 tips that generated by Phylomatic)

References

Bryant, J.A., 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 of the United States of America, 105, 11505-11511.

Morlon, H., Schwilk, D.W., Bryant, J.A., Marquet, P.A., Rebelo, A.G., Tauss, C., Bohannan, B.J.M. & Green, J.L. (2011) Spatial patterns of phylogenetic diversity. Ecology Letters, 14, 141-149.

See Also

phylocom.pd

Examples

#  Please make sure the Phylocom executable file can 
#  be invoked by console by adding the system path for it.
#  res <- phylocom.phylosor(sample.file = "sample", phylo = "phylo")
#