Stemwardness: '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 numeric
SisterSize(tree, tip)
# S3 method for character
SisterSize(tree, tip)
RootNodeDistance(tree, tip)
# S3 method for numeric
RootNodeDistance(tree, tip)
# S3 method for 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.

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.

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. 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).

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. 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.

References

Asher2020TreeTools

Examples

Run this code

# NOT RUN {
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')
# }

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