Description Usage Arguments Details Value Author(s) References Examples
Given a phylogenetic tree, computes the Sackin balance index of that phylogenetic tree.
1 | sackin.index(tree, norm = FALSE)
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tree |
a single phylogenetic tree. It can be entered as a string in Newick format, as a 'phylo' object ( |
norm |
a logical variable that indicates whether the index should be normalized or not. |
The Sackin's index is computed as the sum of the number of ancestors for each leave of the tree.
numeric value.
Lucia Rotger
M. J. Sackin, "Good" and "bad" phenograms. Sys. Zool, 21 (1972), 225-226.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | # 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)
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