Calculate the Kendall-Colijn tree distance, a measure related to the path difference.
KendallColijn(tree1, tree2 = tree1) KCVector(tree)
Trees of class
A tree of class
KendallColijn() returns an array of numerics providing the
distances between each pair of trees in
The Kendall-Colijn distance works by measuring, for each pair of leaves, the distance from the most recent common ancestor of those leaves and the root node. For a given tree, this produces a vector of values recording the distance-from-the-root of each most recent common ancestor of each pair of leaves.
Two trees are compared by taking the Euclidian distance between the respective vectors. This is calculated by taking the square root of the sum of the squares of the differences between the vectors.
This metric emphasizes the position of the root; the path difference instead measures the distance of the last common ancestor of each pair of leaves from the leaves themselves, i.e. the length of the path from one leaf to another.
KCVector: Creates a vector that characterises a rooted tree,
as described in Kendall & Colijn (2016).
Kendall M, Colijn C (2016). “Mapping phylogenetic trees to reveal distinct patterns of evolution.” Molecular Biology and Evolution, 33(10), 2735--2743. doi: 10.1093/molbev/msw124 , https://doi.org/10.1093/molbev/msw124.
is a more sophisticated, if more cumbersome, implementation that supports
lambda > 0, i.e. use of edge lengths in tree comparison.
#>  11.48913#>  9.591663 5.567764 9.949874#> [,1] [,2] [,3] [,4] #> [1,] 0.000000 7.280110 7.874008 4.795832 #> [2,] 7.280110 0.000000 8.185353 7.071068 #> [3,] 7.874008 8.185353 0.000000 7.681146 #> [4,] 4.795832 7.071068 7.681146 0.000000