TreeDist (version 2.9.2)

SPRDist: Approximate the Subtree Prune and Regraft (SPR) distance.

Description

SPRDist() calculates an upper bound on the SPR distance between trees using the heuristic method of deOliveira2008;textualTreeDist. Other approximations are available @e.g. @Hickey2008, @Goloboff2008SPR, @Whidden2018TreeDist.

Usage

SPRDist(tree1, tree2 = NULL, method = "deOliveira", symmetric)
# S3 method for phylo
SPRDist(tree1, tree2 = NULL, method = "deOliveira", symmetric)
# S3 method for list
SPRDist(tree1, tree2 = NULL, method = "deOliveira", symmetric)
# S3 method for multiPhylo
SPRDist(tree1, tree2 = NULL, method = "deOliveira", symmetric)

Value

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

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 Day1985;textualTreeDist.

method

Character specifying which method to use to approximate the SPR distance. Currently defaults to "deOliveira", the only available option; a new method will eventually become the default.

symmetric

Ignored (redundant after fix of phangorn#97).

Author

Martin R. Smith ()

References

See Also

Exact calculation with TBRDist functions USPRDist() and ReplugDist().

phangorn function SPR.dist() employs the deOliveira2008;textualTreeDist algorithm but can crash when sent trees of certain formats, and tends to have a longer running time.

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

Examples

library("TreeTools", quietly = TRUE)

# Compare single pair of trees
SPRDist(BalancedTree(7), PectinateTree(7))

# Compare all pairs of trees        
SPRDist(as.phylo(30:33, 8))

# Compare each tree in one list with each tree in another
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))