R: 'Stemwardness' of a leaf

Stemwardness {TreeTools} | R Documentation

## '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. 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).

`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.

### 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 (martin.smith@durham.ac.uk)

### References

Asher R, Smith MR (2020). “Forthcoming manuscript.” TBC.

### See Also

Other tree characterization functions: `CladisticInfo()`, `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')

[Package TreeTools version 1.3.1 Index]