Calculate length of paths between each pair of vertices within tree

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 phylo, in Preorder.

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()

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

tree <- rtree(6)
plot(tree)
add.scale.bar()
nodelabels()
tiplabels()

PathLengths(tree)
#>    start end     length
#> 1      7   1 2.13032582
#> 2      8   1 2.00095347
#> 3      9   1 1.52283544
#> 4     10   1 0.59876097
#> 5      7   2 2.50773555
#> 6      8   2 2.37836320
#> 7      9   2 1.90024516
#> 8     10   2 0.97617069
#> 9      7   3 1.69600981
#> 10     8   3 1.56663746
#> 11     9   3 1.08851942
#> 12    11   3 0.35672691
#> 13     7   4 1.77075658
#> 14     8   4 1.64138424
#> 15     9   4 1.16326620
#> 16    11   4 0.43147369
#> 17     7   5 0.27758391
#> 18     8   5 0.14821156
#> 19     7   6 0.01307758
#> 20     7   8 0.12937235
#> 21     7   9 0.60749038
#> 22     8   9 0.47811803
#> 23     7  10 1.53156485
#> 24     8  10 1.40219250
#> 25     9  10 0.92407447
#> 26     7  11 1.33928289
#> 27     8  11 1.20991055
#> 28     9  11 0.73179251