| PathLengths {TreeTools} | R Documentation |
Calculate length of paths between each pair of vertices within tree
Description
Given a weighted rooted tree tree, PathLengths() returns the distance
from each vertex to each of its descendant vertices.
Usage
PathLengths(tree, fullMatrix = FALSE)
Arguments
tree |
Original tree of class |
fullMatrix |
Logical specifying return format; see "value" section'. |
Value
If fullMatrix = TRUE, PathLengths() returns a square matrix in
which entry [i, j] denotes the distance from internal node i to the
descendant vertex j.
Vertex pairs without a continuous directed path are denoted NA.
If fullMatrix = FALSE, PathLengths() returns a data.frame with three
columns: start lists the deepest node in each path (i.e. that closest
to the root); end lists the shallowest node (i.e. that closest to a leaf);
length lists the total length of that path.
Author(s)
Martin R. Smith (martin.smith@durham.ac.uk)
See Also
Other tree properties:
ConsensusWithout(),
MatchEdges(),
NSplits(),
NTip(),
NodeNumbers(),
SplitsInBinaryTree(),
TipLabels(),
TreeIsRooted()
Examples
tree <- rtree(6)
plot(tree)
add.scale.bar()
nodelabels()
tiplabels()
PathLengths(tree)