RPANDA (version 1.2)

JSDtree: 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

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)