Calculate the path distance between rooted or unrooted 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 Farris1969TreeDist took the mean squared difference between the elements of each tree's tabulation (Farris, 1973); the method used here is that proposed by Steel1993;textualTreeDist, which takes the square root of this sum. Other precursor measures are described in Williams1971;textualTreeDist and 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 Farris1973TreeDist.
See also
Other tree distances:
JaccardRobinsonFoulds()
,
KendallColijn()
,
MASTSize()
,
MatchingSplitDistance()
,
NNIDist()
,
NyeSimilarity()
,
Robinson-Foulds
,
SPRDist()
,
TreeDistance()
Examples
library("TreeTools")
# Treating the two edges to the root node as distinct
PathDist(BalancedTree(7), PectinateTree(7))
#> [1] 5.656854
# Counting those two edges once
PathDist(UnrootTree(BalancedTree(7)), UnrootTree(PectinateTree(7)))
#> [1] 4.690416
PathDist(BalancedTree(7), as.phylo(0:2, 7))
#> [1] 8.944272 8.124038 8.944272
PathDist(as.phylo(0:2, 7), PectinateTree(7))
#> [1] 7.745967 8.246211 8.124038
PathDist(list(bal = BalancedTree(7), pec = PectinateTree(7)),
as.phylo(0:2, 7))
#> [,1] [,2] [,3]
#> [1,] 8.944272 8.124038 8.944272
#> [2,] 7.745967 8.246211 8.124038
PathDist(as.phylo(30:33, 8))
#> 1 2 3
#> 2 3.872983
#> 3 3.872983 3.464102
#> 4 5.567764 6.928203 6.928203