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, use.na = TRUE)

Arguments

tree

Original tree of class phylo, in Preorder.

fullMatrix

Logical specifying return format; see "value" section`.

use.na

Logical specifying whether to set non-existent paths to NA, or to leave uninitialized. Set to FALSE to maximize performance.

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 use.na is TRUE. 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: Cherries(), ConsensusWithout(), LongBranch(), MatchEdges(), NSplits(), NTip(), NodeNumbers(), SplitsInBinaryTree(), TipLabels(), TreeIsRooted(), Treeness()

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 1.1269270
#> 2      8   1 0.3082923
#> 3      7   2 1.4682141
#> 4      8   2 0.6495795
#> 5      7   3 2.2470673
#> 6      9   3 1.2937119
#> 7     10   3 0.3399792
#> 8      7   4 2.3350161
#> 9      9   4 1.3816607
#> 10    10   4 0.4279280
#> 11    11   4 0.1654539
#> 12     7   5 2.4917303
#> 13     9   5 1.5383748
#> 14    10   5 0.5846422
#> 15    11   5 0.3221681
#> 16     7   6 1.4634807
#> 17     9   6 0.5101252
#> 18     7   8 0.8186347
#> 19     7   9 0.9533555
#> 20     7  10 1.9070881
#> 21     9  10 0.9537327
#> 22     7  11 2.1695622
#> 23     9  11 1.2162068
#> 24    10  11 0.2624741