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 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 |
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')