sackin.index: Computes the Sackin balance index of a phylogenetic tree

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

Description

Given a phylogenetic tree, computes the Sackin balance index of that phylogenetic tree.

Usage

sackin.index(tree, norm = 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 index should be normalized or not.

Details

The Sackin's index is computed as the sum of the number of ancestors for each leave of the tree.

Value

numeric value.

Author(s)

Lucia Rotger

References

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

Examples

# Computation of the Sackin balance index of trees 
# entered in newick format:
sackin.index("(1,2,3,4,5);")
sackin.index("(1,(2,(3,(4,5))));")

# Computation of the Sackin balance index of trees 
# entered as a phylo object:
require(ape)
random.tree = rtree(5,rooted=TRUE)
sackin.index(random.tree)

# Computation of the Sackin balance index 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)
sackin.index(a.g.tree)

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

LuciaRotger/CollessLike documentation built on Oct. 13, 2019, 11:16 a.m.