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(), EdgeRatio(), 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 1.3248956
#> 2      8   1 0.7617968
#> 3      7   2 2.0162235
#> 4      8   2 1.4531247
#> 5      9   2 0.7078273
#> 6      7   3 2.2952045
#> 7      8   3 1.7321056
#> 8      9   3 0.9868082
#> 9      7   4 0.8084836
#> 10    10   4 0.3568527
#> 11    11   4 0.2386353
#> 12     7   5 1.0403711
#> 13    10   5 0.5887402
#> 14    11   5 0.4705228
#> 15     7   6 0.8039540
#> 16    10   6 0.3523231
#> 17     7   8 0.5630988
#> 18     7   9 1.3083962
#> 19     8   9 0.7452974
#> 20     7  10 0.4516309
#> 21     7  11 0.5698483
#> 22    10  11 0.1182174