SPRDist: Approximate Subtree Prune and Regraft distance

In TreeDist: Calculate and Map Distances Between Phylogenetic Trees

Approximate Subtree Prune and Regraft distance

Description

Approximate the Subtree Prune and Regraft (SPR) distance.

Usage

SPRDist(tree1, tree2 = NULL, symmetric = TRUE)

Arguments

tree1, tree2	Trees of class phylo, with leaves labelled identically, or lists of such trees to undergo pairwise comparison. Where implemented, tree2 = NULL will compute distances between each pair of trees in the list tree1 using a fast algorithm based on Day (1985).
symmetric	Logical specifying whether to produce a better heuristic by calculating the minimum of SPRDist(t1, t2) and SPRDist(t2, t1), which are not guaranteed to be equal due to the heuristic nature of the approximation (see phangorn#97). Set to FALSE for the faster approximation, as implemented in "phangorn".

Details

SPRDist() is a wrapper for the function SPR.dist() in the phangorn package. It pre-processes trees to ensure that their internal representation does not cause the SPR.dist() function to crash R, and allows an improved (but slower) symmetric heuristic.

A memory leak is present in phangorn v2.5.5. To avoid a drain on system resources, install the latest version of phangorn with devtools::install_github("KlausVigo/phangorn").

Value

SPRDist() returns a vector or distance matrix of distances between trees.

Author(s)

Martin R. Smith ([e-mail])

See Also

Other tree distances: JaccardRobinsonFoulds(), KendallColijn(), MASTSize(), MatchingSplitDistance(), NNIDist(), NyeSimilarity(), PathDist(), Robinson-Foulds, TreeDistance()

Examples

library("TreeTools", quietly = TRUE)

SPRDist(BalancedTree(7), PectinateTree(7))

SPRDist(BalancedTree(7), as.phylo(0:2, 7))
SPRDist(as.phylo(0:2, 7), PectinateTree(7))

SPRDist(list(bal = BalancedTree(7), pec = PectinateTree(7)),
        as.phylo(0:2, 7))

CompareAll(as.phylo(30:33, 8), SPRDist)

TreeDist documentation built on Oct. 26, 2023, 1:07 a.m.