Calculate length of paths between each pair of vertices within tree
Source:R/PathLengths.R
PathLengths.RdGiven a weighted rooted tree tree, PathLengths() returns the distance
from each vertex to each of its descendant vertices.
Arguments
- tree
Original tree of class
phylo, inPreorder.- 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.
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)
#> start end length
#> 1 7 1 1.0503595
#> 2 8 1 0.2675082
#> 3 7 2 1.5182935
#> 4 8 2 0.7354421
#> 5 9 2 0.5167968
#> 6 7 3 1.2704472
#> 7 8 3 0.4875959
#> 8 9 3 0.2689506
#> 9 7 4 1.2625274
#> 10 10 4 1.0813591
#> 11 11 4 0.5627829
#> 12 7 5 0.8289013
#> 13 10 5 0.6477330
#> 14 11 5 0.1291569
#> 15 7 6 0.4375359
#> 16 10 6 0.2563676
#> 17 7 8 0.7828513
#> 18 7 9 1.0014966
#> 19 8 9 0.2186453
#> 20 7 10 0.1811683
#> 21 7 11 0.6997445
#> 22 10 11 0.5185761