Relative length of internal branches

Treeness (also termed stemminess) is the proportion of a tree's length found on internal branches (Lanyon 1988) . Insofar as external branches do not contain phylogenetic (grouping) signal, trees with a high treeness can be interpreted as containing a higher signal:noise ratio (Phillips and Penny 2003-08) .

Usage

Treeness(tree)

Stemminess(tree)

Arguments

tree

A tree of class phylo, or a list of trees of class list or multiPhylo.

Value

Treeness() returns a numeric vector reporting the treeness of each tree.

References

Lanyon SM (1988). “The Stochastic Mode of Molecular Evolution: What Consequences for Systematic Investigations?” The Auk, 105(3), 565–573. doi:10.1093/auk/105.3.565 .

Phillips MJ, Penny D (2003-08). “The Root of the Mammalian Tree Inferred from Whole Mitochondrial Genomes.” Molecular Phylogenetics and Evolution, 28(2), 171–185. doi:10.1016/S1055-7903(03)00057-5 .

See also

Other tree properties: ConsensusWithout(), LongBranch(), MatchEdges(), NSplits(), NTip(), NodeNumbers(), PathLengths(), SplitsInBinaryTree(), TipLabels(), TreeIsRooted()

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

lowTree <- BalancedTree(6, lengths = c(1, 1, 4, 4, 4, 1, 1, 4, 4, 4))
plot(lowTree)

Treeness(lowTree)
#> [1] 0.1428571
highTree <- BalancedTree(6, lengths = c(6, 6, 1, 1, 1, 6, 6, 1, 1, 1))
plot(highTree)

Treeness(c(lowTree, highTree))
#> [1] 0.1428571 0.8000000