Class CladeHeightMetric

  • All Implemented Interfaces:
    RootedTreeMetric

    public class CladeHeightMetric
    extends java.lang.Object
    implements RootedTreeMetric
    For each clade_j in treeB, find the MRCA_j of the taxa in clade_j in treeA. obviously, if clade_i exists in treeB then clade_i == MRCA_i. Then find the sum of squares of the differences in height: d = sqrt( sum across i[ (height(clade_i) - height(MRCA_i))^2 ] + sum across j[ (height(clade_j) - height(MRCA_j))^2 ] ) The rationale is that if a clade moves then this includes the size of movement across the MRCA node and down again. I.e., a clade that moves from one side of the tree to the other scores the difference between the height of that node and the root and back down to the height of the node in the other tree. +---------A +---------A +-+ +-+ | +---------B | |+--------B + ====> + ++ | +---------C | +--------C +-+ | +---------D +-----------D height(tree1) tmrca(tree2) diff AB 10 10 0 CD 10 12 2 ABCD 12 12 0 height(tree1) tmrca(tree2) diff BC 9 12 3 ABC 10 10 0 ABCD 12 12 0 So the score is sqrt(2^2 + 3^2) = sqrt(13) Scores much less than this: +----------A +----------A + + +-+ | +----------B | | +-B + ====> + +--------+ | +---C | +-C +--------+ | +---D +------------D height(tree1) tmrca(tree2) diff AB 10 10 0 CD 4 12 8 ABCD 12 12 0 height(tree1) tmrca(tree2) diff BC 2 12 10 ABC 10 10 0 ABCD 12 12 0 So the score is sqrt(8^2 + 10^2) = sqrt(164)
    Version:
    $Id$
    Author:
    Andrew Rambaut
    • Constructor Detail

      • CladeHeightMetric

        public CladeHeightMetric()
      • CladeHeightMetric

        public CladeHeightMetric​(java.util.List<Taxon> taxa)
    • Method Detail

      • getMetric

        public double getMetric​(RootedTree tree1,
                                RootedTree tree2)
        Description copied from interface: RootedTreeMetric
        calculates the metric between two rooted trees
        Specified by:
        getMetric in interface RootedTreeMetric
        Parameters:
        tree1 - first tree
        tree2 - second tree
        Returns:
        the tree metric value