Stemwardness: "Stemwardness" of a leaf

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

"Stemwardness" of a leaf

Description

Functions to describe the position of a leaf relative to the root. "Stemmier" leaves ought to exhibit a smaller root-node distance and a larger sister size.

Usage

SisterSize(tree, tip)

## S3 method for class 'numeric'
SisterSize(tree, tip)

## S3 method for class 'character'
SisterSize(tree, tip)

RootNodeDistance(tree, tip)

## S3 method for class 'numeric'
RootNodeDistance(tree, tip)

## S3 method for class 'character'
RootNodeDistance(tree, tip)

RootNodeDist(tree, tip)

Arguments

tree	A tree of class phylo.
tip	Either a numeric specifying the index of a single tip, or a character specifying its label.

Details

RootNodeDistance() calculates the number of nodes between the chosen leaf and the root of tree. This is an unsatisfactory measure, as the range of possible distances is a function of the shape of the tree \insertCiteAsher2020TreeTools. As an example, leaf X1 in the tree ⁠(.,(.,(.,(.,(X1,(a,b))))))⁠ falls outside the clade (a, b) and has a root-node distance of 4, whereas leaf X2 in the tree ⁠(.,((.,(.,.)),(b,(X2,a))))⁠ falls within the clade (a, b), so should be considered more "crownwards", yet has a smaller root-node distance (3).

\insertFig

Stemwardness.pngTreeTools par(mfrow = c(1, 2), mar = rep(0.3, 4)) plot(ape::read.tree(text="(.,(.,(.,(.,(X1,(a,b))))));")) ape::nodelabels(1:4, 9:12) ape::edgelabels(1:2, 11:12)

plot(ape::read.tree(text="(.,((.,(.,.)),(b,(X2,a))));")) ape::nodelabels(1:3, c(9, 12, 13)) ape::edgelabels(1, 12)

SisterSize() measures the number of leaves in the clade that is sister to the chosen leaf, as proposed by \insertCiteAsher2020;textualTreeTools. In the examples above, X1 has a sister size of 2 leaves, whereas X2, which is "more crownwards", has a smaller sister size (1 leaf), as desired.

Value

SisterSize() returns an integer specifying the number of leaves in the clade that is sister to tip. RootNodeDist() returns an integer specifying the number of nodes between tip and the root node of tree.

Author(s)

Martin R. Smith ([e-mail])

References

\insertAllCited

See Also

Other tree characterization functions: CladisticInfo(), Consensus(), J1Index(), TotalCopheneticIndex()

Examples

bal8 <- BalancedTree(8)
pec8 <- PectinateTree(8)

SisterSize(bal8, 3)
SisterSize(pec8, "t3")
SisterSize(RootTree(pec8, "t3"), "t3")

RootNodeDist(bal8, 3)
RootNodeDist(pec8, "t3")
RootNodeDist(RootTree(pec8, "t3"), "t3")

TreeTools documentation built on Sept. 11, 2024, 8:27 p.m.