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Geodesic (BHV) distance between trees

Source: R/BHV.R
BHVDistance.Rd

BHVDistance() returns the geodesic distance between phylogenetic trees with edge lengths in the Billera-Holmes-Vogtmann (BHV) treespace (Billera et al. 2001) , computed with the polynomial-time GTP algorithm of Owen and Provan (2011) .

Usage

BHVDistance(tree1, tree2 = NULL)

BHVDist(tree1, tree2 = NULL)

BHV(tree1, tree2 = NULL)

Arguments

tree1, tree2

A phylo tree, a multiPhylo object, or a list of phylo trees, each carrying edge.length. All trees across both arguments must share the same leaf labels. tree2 may be omitted when tree1 is a collection, in which case all pairwise distances within tree1 are returned.

Value

BHVDistance() returns distances between the input trees:

  • If both inputs are single trees, the return value is a single non-negative number.

  • When comparing a tree to a collection of trees, the return value is a named numeric vector with one entry per tree in the collection.

  • If tree2 is omitted, or is identical to tree1, the return value is a stats::dist object of all pairwise distances.

  • If tree1 and tree2 are different collections, the return value comprises a numeric matrix with rows corresponding to tree1 and columns to tree2.

References

Billera LJ, Holmes SP, Vogtmann K (2001). “Geometry of the space of phylogenetic trees.” Advances in Applied Mathematics, 27(4), 733–767. doi:10.1006/aama.2001.0759 .

Owen M, Provan JS (2011). “A fast algorithm for computing geodesic distances in tree space.” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(1), 2–13. doi:10.1109/TCBB.2010.3 .

See also

Other BHV summaries: BHVMean()

Examples

set.seed(2)
trees <- lapply(1:4, function(i) 
  TreeTools::RandomTree(8, root = TRUE, lengths = runif)
)
t1 <- trees[[1]]
t2 <- trees[[2]]

BHVDistance(t1, t2)                  # scalar
#> [1] 2.742226
BHVDistance(t1, trees)               # named vector
#> [1] 0.000000 2.742226 3.088498 3.158640
BHVDistance(trees)                   # dist (pairwise)
#>          1        2        3
#> 2 2.742226                  
#> 3 3.088498 3.094400         
#> 4 3.158640 3.187792 3.344174
BHVDistance(trees[1:2], trees[3:4])  # matrix
#>          [,1]     [,2]
#> [1,] 3.088498 3.158640
#> [2,] 3.094400 3.187792