balance.indices: Computes Colles-like, Sackin and cophenetic balance indices...

In CollessLike: Distribution and Percentile of Sackin, Cophenetic and Colless-Like Balance Indices of Phylogenetic Trees

Description

Given a phylogenetic tree, computes Colles-like, Sackin and cophenetic balance indices of that tree.

Usage

balance.indices(tree, norm = FALSE, binary.Colless = FALSE)

Arguments

tree	a single phylogenetic tree. It can be entered as a string in Newick format, as a 'phylo' object (ape package) or as an 'igraph' object (igraph package).
norm	a logical variable that indicates whether the indices should be normalized or not.
binary.Colless	a logical variable FALSE by default. If is TRUE then the classical Colless index is computed (only for binary trees).

Details

The Colless-like index is the generalization of the Colless' index for non-binary trees (see Mir et al. , 2018).

The Sackin's index is computed as the sum of the number of ancestors for each leave of the tree (see Mir et al. , 2013).

The cophenetic index is computed as the sum of the depths of the least common ancestor (LCA) of every pair of leaves of the tree(see Sackin et al, 1972).

Value

A numeric vector with the three computed balance indices of the tree: Colless-like, Sackin and Cophenetic values.

Author(s)

Lucia Rotger

References

A. Mir, F. Rossello, L.Rotger, Sound Colless-like balance indices for multifurcating phylogenetic trees.PloS ONE 13 (2018), e0203401.

A. Mir, F. Rossello, L.Rotger, A new balance index for phylogenetic trees. Mathematical Biosciences 241 (2013), 125-136.

M. J. Sackin, "Good" and "bad" phenograms. Sys. Zool, 21 (1972), 225-226.

Examples

# Computation of the Colless-Like, Sackin and Cophenetic 
# balance indices of trees entered in newick format:
balance.indices("(1,2,3,4,5);")
balance.indices("(1,(2,(3,(4,5))));")

# Computation of the Colless-Like, Sackin and Cophenetic
# balance indices of a tree entered as a phylo object:
require(ape)
random.tree = rtree(5,rooted=TRUE)
balance.indices(random.tree)

# Computation of the Colless-Like, Sackin and Cophenetic 
# balance indices of a tree entered as a igraph object.
# The tree is randomly generated from all trees with 5
# leaves following the alpha-gamma model with alpha=0.5
# and gamma=0.3.
a.g.tree = a.g.model(5,0.5,0.3)
balance.indices(a.g.tree)

# All of them can be normalized (values between 0 and 1)
balance.indices("(1,2,3,4,5);",norm=TRUE)
balance.indices("(1,(2,(3,(4,5))));",norm=TRUE)
balance.indices(random.tree,norm=TRUE)
balance.indices(a.g.tree,norm=TRUE)

CollessLike documentation built on Oct. 30, 2019, 12:05 p.m.