Skip to contents

Apply all available tree statistics to a single tree

Source: R/calc_all_stats.R
calc_all_stats.Rd

this function applies all tree statistics available in this package to a single tree, being:

  • gamma

  • Sackin

  • Colless

  • corrected Colless

  • quadratic Colless

  • Aldous' beta statistic

  • Blum

  • crown age

  • tree height

  • Pigot's rho

  • number of lineages

  • nLTT with empty tree

  • phylogenetic diversity

  • avgLadder index

  • cherries

  • double cherries

  • ILnumber

  • pitchforks

  • stairs

  • stairs2

  • laplacian spectrum

  • B1

  • B2

  • area per pair (aPP)

  • average leaf depth (aLD)

  • I statistic

  • ewColless

  • max Delta Width (maxDelW)

  • maximum of Depth

  • variance of Depth

  • maximum Width

  • Rogers

  • total Cophenetic distance

  • symmetry Nodes

  • mean of pairwise distance (mpd)

  • variance of pairwise distance (vpd)

  • Phylogenetic Species Variability (psv)

  • mean nearest taxon distance (mntd)

  • J statistic of entropy

  • rquartet index

  • Wiener index

  • max betweenness

  • max closeness

  • diameter, without branch lenghts

  • maximum eigen vector value

  • mean branch length

  • variance of branch length

  • mean external branch length

  • variance of external branch length

  • mean internal branch length

  • variance of internal branch length

  • number of imbalancing steps

  • j_one statistic

  • treeness statistic

For the Laplacian spectrum properties, four properties of the eigenvalue distribution are returned: 1) asymmetry, 2) peakedness, 3) log(principal eigenvalue) and 4) eigengap. Please notice that for some very small or very large trees, some of the statistics can not be calculated. The function will report an NA for this statistic, but will not break, to facilitate batch analysis of large numbers of trees.

Usage

calc_all_stats(phylo, normalize = FALSE)

Arguments

phylo

phylo object

normalize

if set to TRUE, results are normalized (if possible) under either the Yule expectation (if available), or the number of tips

Value

List with statistics