computeSpectralStats: Spectra of a rooted phylo tree.

In Leonardini/treeCentrality: Computation of Network Science Statistics on Trees in Linear Time

Description

computeSpectralStats computes various spectra of a rooted binary phylo tree.

Usage

computeSpectralStats(tree, weight = c(FALSE, TRUE), adj = c(FALSE,
  TRUE), norm = FALSE, dist = FALSE, full = FALSE, maxOnly = TRUE,
  unitMean = FALSE)

Arguments

tree	A tree of class phylo. The tree should be binary and rooted; if it is not, it will be coerced into a rooted tree using root and/or binarized using multi2di.
weight	A logical vector; a TRUE (FALSE) entry means the branch lengths are (not) taken into account.
adj	A logical vector; a TRUE (FALSE) entry means the adjacency (Laplacian) spectrum is computed.
norm	A logical vector; a TRUE (FALSE) entry means the Laplacian is (not) normalized.
dist	A logical vector; a TRUE (FALSE) entry means the distance (regular) matrix is used.
full	A logical vector; a TRUE (FALSE) entry means the full (leaf-leaf) distance matrix is used.
maxOnly	A logical scalar; if TRUE, only the maximum value of each vector is returned.
unitMean	A logical scalar; if TRUE, the tree's branch lengths are scaled to unit mean beforehand.

Value

A named list containing the specified spectra (or only their maximum values).

See Also

Other drivers for computing summary statistics: computeBasicStats, computeLMStats, computeNetworkStats, rankDiscriminatoryStats

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