spectR: Spectral density plot of a phylogeny

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

Spectral density plot of a phylogeny

Description

Computes the spectra of eigenvalues for the modified graph Laplacian of a phylogenetic tree, identifies the spectral gap, then convolves the eigenvalues with a Gaussian kernel, and plots them alongside all eigenvalues ranked in descending order.

Usage

spectR(phylo, meth=c("standard"),zero_bound=FALSE)

Arguments

phylo	an object of type 'phylo' (see ape documentation)
meth	the method used to compute the spectral density, which can either be "standard" or "normal". If set to "standard", computes the unnormalized version of the spectral density. If set to "normal", computes the spectral density normalized to the degree matrix (see the associated paper for an explanation)
zero_bound	if false, eigenvalues less than one are discarded

Details

Note that the eigengap should in principle be computed with the "standard" option

Value

a list with the following components:

eigenvalues	the vector of eigenvalues
principal_eigenvalue	the largest (or principal) eigenvalue of the spectral density profile
asymmetry	the skewness of the spectral density profile
peak_height	the largest y-axis value of the spectral density profile
eigengap	the position of the largest difference between eigenvalues, giving the number of modalities in the tree

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

plot_spectR, JSDtree, BICompare

Examples

data(Cetacea)
spectR(Cetacea,meth="standard",zero_bound=FALSE)

hmorlon/PANDA documentation built on Jan. 13, 2025, 5:35 a.m.