Class UPGMALinkage


  • public class UPGMALinkage
    extends Linkage
    Unweighted Pair Group Method with Arithmetic mean (also known as average linkage). The distance between two clusters is the mean distance between all possible pairs of nodes in the two clusters.

    In bioinformatics, UPGMA is used for the creation of phenetic trees (phenograms). UPGMA assumes a constant rate of evolution (molecular clock hypothesis), and is not a well-regarded method for inferring relationships unless this assumption has been tested and justified for the data set being used.

    Author:
    Haifeng Li
    • Constructor Summary

      Constructors 
      Constructor Description
      UPGMALinkage​(double[][] proximity)
      Constructor.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void merge​(int i, int j)
      Merge two clusters into one and update the proximity matrix.
      java.lang.String toString()  
      • Methods inherited from class smile.clustering.linkage.Linkage

        d, size
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    • Constructor Detail

      • UPGMALinkage

        public UPGMALinkage​(double[][] proximity)
        Constructor.
        Parameters:
        proximity - the proximity matrix to store the distance measure of dissimilarity. To save space, we only need the lower half of matrix.
    • Method Detail

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • merge

        public void merge​(int i,
                          int j)
        Description copied from class: Linkage
        Merge two clusters into one and update the proximity matrix.
        Specified by:
        merge in class Linkage
        Parameters:
        i - cluster id.
        j - cluster id.