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Chapter Contents
Chapter Introduction
NAG Toolbox

NAG Toolbox: nag_mv_cluster_hier (g03ec)


    1  Purpose
    2  Syntax
    7  Accuracy
    9  Example


nag_mv_cluster_hier (g03ec) performs hierarchical cluster analysis.


[d, ilc, iuc, cd, iord, dord, ifail] = g03ec(method, n, d)
[d, ilc, iuc, cd, iord, dord, ifail] = nag_mv_cluster_hier(method, n, d)


Given a distance or dissimilarity matrix for n objects (see nag_mv_distance_mat (g03ea)), cluster analysis aims to group the n objects into a number of more or less homogeneous groups or clusters. With agglomerative clustering methods, a hierarchical tree is produced by starting with n clusters, each with a single object and then at each of n-1 stages, merging two clusters to form a larger cluster, until all objects are in a single cluster. This process may be represented by a dendrogram (see nag_mv_cluster_hier_dendrogram (g03eh)).
At each stage, the clusters that are nearest are merged, methods differ as to how the distances between the new cluster and other clusters are computed. For three clusters i, j and k let ni, nj and nk be the number of objects in each cluster and let dij, dik and djk be the distances between the clusters. Let clusters j and k be merged to give cluster jk, then the distance from cluster i to cluster jk, di.jk can be computed in the following ways.
1. Single link or nearest neighbour : di.jk = mindij,dik .
2. Complete link or furthest neighbour : di.jk=maxdij,dik.
3. Group average : di.jk= njnj+nk dij+ nknj+nk dik.
4. Centroid : di.jk= njnj+nk dij+ nknj+nk dik- njnk nj+nk 2djk.
5. Median : di.jk=12dij+12dik-14djk.
6. Minimum variance : di.jk=ni+njdij+ni+nkdik-nidjk/ni+nj+nk.
For further details see Everitt (1974) or Krzanowski (1990).
If the clusters are numbered 1,2,,n then, for convenience, if clusters j and k, j<k, merge then the new cluster will be referred to as cluster j. Information on the clustering history is given by the values of j, k and djk for each of the n-1 clustering steps. In order to produce a dendrogram, the ordering of the objects such that the clusters that merge are adjacent is required. This ordering is computed so that the first element is 1. The associated distances with this ordering are also computed.


Everitt B S (1974) Cluster Analysis Heinemann
Krzanowski W J (1990) Principles of Multivariate Analysis Oxford University Press


Compulsory Input Parameters

1:     method int64int32nag_int scalar
Indicates which clustering method is used.
Single link.
Complete link.
Group average.
Minimum variance.
Constraint: method=1, 2, 3, 4, 5 or 6.
2:     n int64int32nag_int scalar
n, the number of objects.
Constraint: n2.
3:     dn×n-1/2 – double array
The strictly lower triangle of the distance matrix. D must be stored packed by rows, i.e., d i-1 i-2 /2+j , i>j must contain dij.
Constraint: di0.0, for i=1,2,,nn-1/2.

Optional Input Parameters


Output Parameters

1:     dn×n-1/2 – double array
Is overwritten.
2:     ilcn-1 int64int32nag_int array
ilcl contains the number, j, of the cluster merged with cluster k (see iuc), j<k, at step l, for l=1,2,,n-1.
3:     iucn-1 int64int32nag_int array
iucl contains the number, k, of the cluster merged with cluster j, j<k, at step l, for l=1,2,,n-1.
4:     cdn-1 – double array
cdl contains the distance djk, between clusters j and k, j<k, merged at step l, for l=1,2,,n-1.
5:     iordn int64int32nag_int array
The objects in dendrogram order.
6:     dordn – double array
The clustering distances corresponding to the order in iord. dordl contains the distance at which cluster iordl and iordl+1 merge, for l=1,2,,n-1. dordn contains the maximum distance.
7:     ifail int64int32nag_int scalar
ifail=0 unless the function detects an error (see Error Indicators and Warnings).

Error Indicators and Warnings

Errors or warnings detected by the function:
On entry,method1, 2, 3, 4, 5 or 6,
On entry,di<0.0 for some i=1,2,,nn-1/2.
A true dendrogram cannot be formed because the distances at which clusters have merged are not increasing for all steps, i.e., cdl<cdl-1 for some l=2,3,,n-1. This can occur for the median and centroid methods.
An unexpected error has been triggered by this routine. Please contact NAG.
Your licence key may have expired or may not have been installed correctly.
Dynamic memory allocation failed.


For method3 slight rounding errors may occur in the calculations of the updated distances. These would not normally significantly affect the results, however there may be an effect if distances are (almost) equal.
If at a stage, two distances dij and dkl, (i<k) or (i=k), and j<l, are equal then clusters k and l will be merged rather than clusters i and j. For single link clustering this choice will only affect the order of the objects in the dendrogram. However, for other methods the choice of kl rather than ij may affect the shape of the dendrogram. If either of the distances dij and dkl is affected by rounding errors then their equality, and hence the dendrogram, may be affected.

Further Comments

The dendrogram may be formed using nag_mv_cluster_hier_dendrogram (g03eh). Groupings based on the clusters formed at a given distance can be computed using nag_mv_cluster_hier_indicator (g03ej).


Data consisting of three variables on five objects are read in. Euclidean squared distances based on two variables are computed using nag_mv_distance_mat (g03ea), the objects are clustered using nag_mv_cluster_hier (g03ec) and the dendrogram computed using nag_mv_cluster_hier_dendrogram (g03eh). The dendrogram is then printed.
function g03ec_example

fprintf('g03ec example results\n\n');

x = [1, 5, 2;
     2, 1, 1;
     3, 4, 3;
     4, 1, 2;
     5, 5, 0];
[n,m]  = size(x);

isx    = ones(m,1,'int64');
isx(1) = int64(0);
s      = ones(m,1);
ld     = (n*(n-1))/2;
d      = zeros(ld,1);

% Compute the distance matrix
update = 'I';
dist = 'S';
scal = 'U';
[s, d, ifail] = g03ea( ...
		       update, dist, scal, x, isx, s, d);

% Clustering method
method = int64(5);
% Perform clustering
n      = int64(n);
[d, ilc, iuc, cd, iord, dord, ifail] = ...
  g03ec(method, n, d);

row = {'A'; 'B'; 'C'; 'D'; 'E'};
fprintf('  Distance   Clusters Joined\n\n');
for i = 1:n-1
  fprintf('%10.3f     %s %s\n', cd(i), row{ilc(i)}, row{iuc(i)})

g03ec example results

  Distance   Clusters Joined

     1.000     B D
     2.000     A C
     6.500     A E
    14.125     A B

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Chapter Contents
Chapter Introduction
NAG Toolbox

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