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Approximate the Subtree Prune and Regraft (SPR) distance.

Source: R/tree_distance_spr.R
SPRDist.Rd

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 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 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).

Value

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

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()

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

library("TreeTools", quietly = TRUE)

# Compare single pair of trees
SPRDist(BalancedTree(7), PectinateTree(7))
#> [1] 2

# Compare all pairs of trees        
SPRDist(as.phylo(30:33, 8))
#>   1 2 3 4
#> 1   1 1 1
#> 2 1   1 1
#> 3 1 1   1
#> 4 1 1 1  

# Compare each tree in one list with each tree in another
SPRDist(BalancedTree(7), as.phylo(0:2, 7))
#> [1] 2 2 2
SPRDist(as.phylo(0:2, 7), PectinateTree(7))
#> [1] 1 2 2

SPRDist(list(bal = BalancedTree(7), pec = PectinateTree(7)),
        as.phylo(0:2, 7))
#>     [,1] [,2] [,3]
#> bal    2    2    2
#> pec    1    2    2