Package 'TBRDist'

Calculate rSPR distance between rooted trees

Description

Calculate rooted Subtree Prune-and-Regraft (rSPR) distances between pairs of rooted binary trees using the algorithms of Whidden, Beiko & Zeh (2013).

Usage

RSPRDist(
  tree1,
  tree2 = NULL,
  allPairs = is.null(tree2),
  checks = TRUE,
  approx = FALSE,
  maf = FALSE
)

Arguments

tree1, tree2	Trees of class phylo, or lists thereof. All trees must be rooted and bear identical sets of tip labels.
allPairs	Logical; if TRUE, compare each tree in tree1 with each tree in tree2; if FALSE, compare corresponding pairs. Defaults to TRUE when tree2 is not supplied.
checks	Logical; validate tree labels and dimensions before computation. Set FALSE at your peril—improper input is likely to crash R.
approx	Logical; if TRUE return the linear-time 3-approximation instead of the exact distance.
maf	Logical; if TRUE return the maximum agreement forest alongside the exact distance (implies approx = FALSE).

Details

This function wraps the rspr C++ library by Chris Whidden. It handles rooted trees and is substantially more efficient than USPRDist() for large trees: it can handle pairs with 200+ leaves and distances > 50.

Note that these distances are NP-hard to compute exactly; running time scales as O(2^k n) where k is the rSPR distance and n is the number of leaves. The built-in cluster decomposition (enabled by default) provides a large practical speedup. Use approx = TRUE for a guaranteed linear-time 3-approximation.

Input trees must be rooted. An error is raised if any tree is unrooted.

Value

By default, an integer vector of rSPR distances (one per tree pair), or a dist object when allPairs = TRUE and tree2 = NULL.

If maf = TRUE, a named list with elements:

exact

Integer vector of rSPR distances.

maf_1, maf_2

Character vectors giving the maximum agreement forest for each pair of trees, expressed as space-separated Newick components.

References

Whidden C, Beiko RG, Zeh N (2013). Fixed-Parameter Algorithms for Maximum Agreement Forests. SIAM Journal on Computing 42:1431–1466. doi:10.1137/110845045

Whidden C, Zeh N, Beiko RG (2014). Supertrees based on the subtree prune-and-regraft distance. Systematic Biology 63:566–581. doi:10.1093/sysbio/syu023

See Also

USPRDist() for unrooted trees.

Examples

library(ape)
set.seed(1)
tree1 <- rtree(8)
tree2 <- rtree(8)
tree1$tip.label <- tree2$tip.label <- paste0("t", 1:8)

RSPRDist(tree1, tree2)

# All pairwise distances among a list of trees
trees <- c(tree1, tree2)
RSPRDist(trees)

# Fast 3-approximation
RSPRDist(tree1, tree2, approx = TRUE)

# With maximum agreement forest
RSPRDist(tree1, tree2, maf = TRUE)

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Calculate SPR, TBR and Replug distances on unrooted trees

Description

Calculate SPR, TBR and Replug distances on unrooted trees, and the information content of the maximum agreement forest.

Usage

USPRDist(
  tree1,
  tree2 = NULL,
  allPairs = is.null(tree2),
  checks = TRUE,
  useTbrApproxEstimate = TRUE,
  useTbrEstimate = TRUE,
  useReplugEstimate = TRUE
)

ReplugDist(
  tree1,
  tree2 = NULL,
  allPairs = is.null(tree2),
  checks = TRUE,
  maf = FALSE
)

TBRDist(
  tree1,
  tree2 = NULL,
  allPairs = is.null(tree2),
  checks = TRUE,
  maf = FALSE,
  countMafs = FALSE,
  printMafs = FALSE,
  exact = maf,
  approximate = !exact,
  optimize = TRUE,
  protectB = TRUE
)

MAFInfo(tree1, tree2 = tree1, exact = FALSE)

Arguments

tree1, tree2	Trees of class phylo, or lists thereof.
allPairs	Logical; if TRUE, compare each tree in tree1 with each tree in tree2; if FALSE, compare each tree in tree1 only with the tree at the corresponding index in tree2. If tree2 is not specified, each tree in tree1 will be compared with each other tree in tree1.
checks	Logical specifying whether to check that trees are properly formatted and labelled. Specify FALSE at your peril, as improper input is likely to crash R.
useTbrApproxEstimate, useTbrEstimate, useReplugEstimate	Logical specifying whether to use approximate TBR distance, TBR distance or Replug distance to help estimate the SPR distance.
maf	Logical specifying whether to report a maximum agreement forest corresponding to the optimal score.
countMafs	Logical specifying whether to count the number of maximum agreement forests found.
printMafs	Logical specifying whether to print maximum agreement forests to stdout whilst counting. Use capture.output(TBRDist(tree1, tree2, printMafs = TRUE)) to access these in R.
exact	Logical specifying whether to calculate the exact TBR distance.
approximate	Logical specifying whether to calculate the approximate TBR distance. By default, is set to the opposite of exact; either approximate or exact should usually be set to TRUE if a distance is required.
optimize	Logical specifying whether to use the default optimizations.
protectB	Logical specifying whether to use the 'PROTECT_B' optimization. Overrides value inherited from optimize.

Details

Note that these distances are NP-hard to compute, so the running time of the algorithms used in this software scale exponentially with the distance computed. The version of 'uspr' linked in this package is aimed at trees with up to 50 leaves and uSPR distances up to 14.

If you are interested in comparing rooted trees in terms of SPR operations, you should use 'rspr' instead. 'rspr' is also much more efficient and can easily handle pairs of binary rooted trees with 200+ leaves and distances > 50. rspr is not yet incorporated in this R package; please contact the maintainer if this would be useful to you.

Value

USPRDist() returns a vector of SPR distances between each pair of unrooted trees.

ReplugDist() returns a vector of Replug distances between each pair of trees, or (if maf = TRUE) a named list whose second and third elements list a vector of maximum agreement forests for each pair of trees.

TBRDist() returns a named list, each element of which bears a vector corresponding to the requested value for each tree pair. If only the exact value is requested (exact = TRUE), an unnamed vector of distances is returned.

MAFInfo() returns the information content of the maximum agreement forest, in bits. This is defined as the sum of the phylogenetic information content of each constituent subtree, plus the entropy of the clusters implied by the division of the tree into subtrees. Note that as there is no guarantee that the most informative MAF will be encountered, this measure is approximate only. exact will only serve to guarantee that a MAF corresponding to the exact TBR distance is among those sampled.

Author(s)

Algorithms implemented by Chris Whidden ([email protected])

R wrappers by Martin R. Smith ([email protected])

References

If you use these functions in your research, please cite:

• Chris Whidden and Frederick A. Matsen IV. Calculating the Unrooted Subtree-Prune-and-Regraft Distance. arXiv:1511.07529.

Examples

tree1 <- TreeTools::BalancedTree(6)
tree2 <- TreeTools::PectinateTree(6)

# SPR distance
USPRDist(tree1, tree2)

# Replug distance
ReplugDist(tree1, tree2)
ReplugDist(tree1, tree2, maf = TRUE)

# TBR distance between two trees
TBRDist(tree1, tree2, exact = TRUE)

# Compare a list against one tree, using approximate distances
TBRDist(list(tree1, tree2), tree2, exact = FALSE)

# Compare all pairs in two lists
TBRDist(list(tree1, tree2), list(tree1, tree2, tree2), allPairs = TRUE,
        exact = FALSE)

# Compare each tree in a list against each other
TBRDist(list(one = tree1, two = tree2, twoAgain = tree2))

# Compare each pair in two lists
TBRDist(list(tree1, tree2, tree2),
        list(tree2, tree1, tree2),
        exact = TRUE, approximate = TRUE, countMafs = TRUE)

# Capture maximum agreement forests
mafs <- capture.output(TBRDist(tree1, tree2, approximate = FALSE,
                        printMafs = TRUE))
head(mafs)

MAFInfo(tree1, tree2)
MAFInfo(list(tree2, tree1), list(tree1, tree2))

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