SOM Toolbox | Online documentation | http://www.cis.hut.fi/projects/somtoolbox/ |

** [Z,order,Md] = som_linkage(sM,varargin)**

SOM_LINKAGE Make a hierarchical linkage of the SOM map units. [Z,order,Dist] = som_linkage(sM, [[argID,] value, ...]) Z = som_linkage(sM); Z = som_linkage(D,'complete'); Z = som_linkage(sM,'single','ignore',find(~som_hits(sM,D))); Z = som_linkage(sM,pdist(sM.codebook,'mahal')); som_dendrogram(Z); Input and output arguments ([]'s are optional): sM (struct) map or data struct to be clustered (matrix) size dlen x dim, a data set: the matrix must not contain any NaN's! [argID, (string) See below. The values which are unambiguous can value] (varies) be given without the preceeding argID. Z (matrix) size dlen-1 x 3, the linkage info Z(i,1) and Z(i,2) hold the indeces of clusters combined on level i (starting from bottom). The new cluster has index dlen+i. The initial cluster index of each unit is its linear index in the original data matrix. Z(i,3) is the distance between the combined clusters. See LINKAGE function in the Statistics Toolbox. The ignored samples are listed at the end of the Z-matrix and have Z(*,3) == Inf Dist (matrix) size dlen x dlen, pairwise distance matrix Here are the valid argument IDs and corresponding values. The values which are unambiguous (marked with '*') can be given without the preceeding argID. 'linkage' *(string) the linkage criteria to use: 'single' (the default), 'average' or 'complete' 'topol' *(struct) topology struct 'connect' *(string) 'neighbors' or 'any' (default), whether the connections should be allowed only between neighbors or between any vectors (matrix) size dlen x dlen indicating the connections between vectors (scalar) the N-neighborhood upto which the connections should be formed (implies 'neighbors') 'ignore' (vector) the units/vectors which should be ignored 'dist' (matrix) size dlen x dlen, pairwise distance matrix to be used instead of euclidian distances (vector) as the output of PDIST function (scalar) distance norm to use (euclidian = 2) 'mask' (vector) size dim x 1, the search mask used to weight distance calculation. By default sM.mask or a vector of ones is used. Note that together 'connect'='neighbors' and 'ignore' may form areas on the map which will never be connected: connections across the ignored map units simply do not exist. See also KMEANS_CLUSTERS, LINKAGE, PDIST, DENDROGRAM.