PathDist function

Path distance

Calculate the path distance between rooted or unrooted trees.

PathDist(tree1, tree2 = NULL)

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.

Returns

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

Details

This function is a faster alternative to the function path.dist() in the phangorn package, which can crash if the internal representation of trees does not conform to certain (unspecified) expectations, and which treats all trees as unrooted.

The path distance is calculated by tabulating the cladistic difference (= topological distance) between each pair of tips in each tree. A precursor to the path distance \insertCite Farris1969TreeDist

took the mean squared difference between the elements of each tree's tabulation (Farris, 1973); the method used here is that proposed by \insertCite Steel1993;textualTreeDist, which takes the square root of this sum. Other precursor measures are described in \insertCite Williams1971;textualTreeDist and \insertCite Phipps1971;textualTreeDist.

If a root node is present, trees are treated as rooted. To avoid counting the root edge twice, use UnrootTree(tree) before calculating the path distance.

Use of the path distance is discouraged as it emphasizes shallow relationships at the expense of deeper (and arguably more fundamental) relationships \insertCite Farris1973TreeDist.

Examples

library("TreeTools")

# Treating the two edges to the root node as distinct
PathDist(BalancedTree(7), PectinateTree(7))

# Counting those two edges once
PathDist(UnrootTree(BalancedTree(7)), UnrootTree(PectinateTree(7)))

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

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

PathDist(as.phylo(30:33, 8))

References

\insertAllCited

See Also

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

Author(s)

Martin R. Smith

(martin.smith@durham.ac.uk)