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, method=c("standard"))
Arguments
phylo
an object of type 'phylo' (see ape documentation)
method
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)
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
peakedness1
the kurtosis of the spectral density profile
peakedness2
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
Details
Note that the eigengap should in principle be computed with the "standard" option
References
Lewitus, E., Morlon, H., Characterizing and comparing phylogenies from their Laplacian spectrum, bioRxiv doi: http://dx.doi.org/10.1101/026476