computeSpectrum: Compute the spectrum (eigenvalues) of a matrix representing a...

Description Usage Arguments See Also

View source: R/Spectra.R

Description

computeSpectrum computes the spectrum of a specified matrix of a phylogenetic tree

Usage

1
computeSpectrum(tree, weight, dist, full, lap, norm)

Arguments

tree

A phylo tree; needs to be binary and rooted.

weight

A logical scalar; if TRUE, branch lengths are used; if a root edge is present, it is ignored!

dist

A logical scalar; if TRUE, the distance matrix is computed.

full

A logical scalar; if TRUE, the node-node distances are used, otherwise, the leaf-leaf ones; ignored if dist = FALSE.

lap

A logical scalar; if TRUE, the Laplacian matrix is computed (defined as diag(rowSums(M))-M for a matrix M).

norm

A logical scalar; if TRUE, the Laplacian is a normalized one (i.e. the diagonal is 1); ignored if lap = FALSE.

See Also

Other functions used to compute tree spectra: computeMatrix


Leonardini/treeCentrality documentation built on April 7, 2020, 3:18 p.m.