Approximate the Subtree Prune and Regraft (SPR) distance.

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'.

Value

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

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').

Examples

library('TreeTools', quietly = TRUE, warn.conflicts = FALSE)

SPRDist(BalancedTree(7), PectinateTree(7))
#> spr 
#>   1 

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

CompareAll(as.phylo(30:33, 8), SPRDist)
#>   1 2 3 4
#> 1   1 1 1
#> 2 1   1 1
#> 3 1 1   1
#> 4 1 1 1