| spectR_t {RPANDA} | R Documentation |
Spectral density plot of phylogenetic trait data
Description
Computes the spectra of eigenvalues for the modified graph Laplacian of a phylogenetic tree with associated tip data, convolves the eigenvalues with a Gaussian kernel and plots the density profile of eigenvalues, and estimates the summary statistics of the profile.
Usage
spectR_t(phylo, dat, draw=F)
Arguments
phylo |
an object of type 'phylo' (see ape documentation) |
dat |
a vector of trait data associated with the tips of the phylo object; tips and trait data should be aligned |
draw |
if true, the spectral density profile of the phylogenetic trait data is plotted |
Value
a list with the following components:
eigenvalues |
the vector of eigenvalues |
splitter |
the largest (or principal) eigenvalue of the spectral density profile |
fragmenter |
the skewness of the spectral density profile |
tracer |
the largest y-axis value of the spectral density profile |
Author(s)
E Lewitus
References
Lewitus, E., Morlon, H. (2019) Characterizing and comparing phylogenetic trait data from their normalized Laplacian spectrum, bioRxiv doi: https://doi.org/10.1101/654087
Examples
tr<-rtree(10)
dat<-runif(10,1,2)
spectR_t(tr,dat,draw=TRUE)