| JSDtree {RPANDA} | R Documentation |
Jensen-Shannon distance between phylogenies
Description
Computes the Jensen-Shannon distance metric between spectral density profiles of phylogenies.
Usage
JSDtree(phylo,meth=c("standard"))
Arguments
phylo |
a list of objects of type 'phylo' (see ape documentation) |
meth |
the method used to compute the spectral density, which can either be "standard", "normal1", or "normal2". if set to "normal1", computes the spectral density normalized to the degree matrix. if set to "normal2", computes the spectral density normalized to the number of eigenvalues. if set to "standard", computes the unnormalized version of the spectral density (see the associated paper for an explanation) |
Value
a matrix providing the Jensen-Shannon distance values between phylogeny pairs
Author(s)
E Lewitus
References
Lewitus, E., Morlon, H., Characterizing and comparing phylogenies from their Laplacian spectrum, bioRxiv doi: http://dx.doi.org/10.1101/026476
See Also
JSDtree_cluster, spectR, BICompare
Examples
trees<-TESS::tess.sim.age(n=20,age=10,0.15,0.05,MRCA=TRUE)
JSDtree(trees)