SPRDist function

Approximate the Subtree Prune and Regraft (SPR) distance.

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

SPRDist(tree1, tree2 = NULL, method = "deOliveira", symmetric)

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

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

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

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 \insertCite 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).

Returns

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

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))

References

\insertAllCited

See Also

Exact calculation with list("TBRDist")

functions USPRDist() and ReplugDist().

phangorn function SPR.dist() employs the \insertCite 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()

Author(s)

Martin R. Smith

(martin.smith@durham.ac.uk)