calculate dunn index matrix?

Hi I have a big matrix and woulk like to calculate dunn index for that. I have seen dunn index function in Matworks but unfortunatly it did not work on my matrix. Please let me know your comments and also if you have any example

Answer 1

[BhaTTa]

To calculate the Dunn index manually, you need to follow these steps:

1. Determine the minimum distance between observations in different clusters (inter-cluster distance).
2. Determine the maximum diameter (the largest distance between any two points) of all the clusters (intra-cluster distance).
3. Calculate the Dunn index as the ratio of the minimum inter-cluster distance to the maximum intra-cluster distance.

Here's a simple example of how you might implement this in MATLAB. This example assumes you have a dataset X and the cluster assignments idx for each observation in X.

function dunnIndex = calculateDunnIndex(X, idx)
    uniqueClusters = unique(idx);
    nClusters = length(uniqueClusters);
    
    % Calculate inter-cluster distances
    minInterClusterDistance = inf;
    for i = 1:nClusters
        for j = i+1:nClusters
            clusterIDistance = pdist2(X(idx==uniqueClusters(i),:), X(idx==uniqueClusters(j),:), 'euclidean', 'Smallest', 1);
            minInterClusterDistance = min(minInterClusterDistance, min(clusterIDistance));
        end
    end
    
    % Calculate intra-cluster distances (diameters)
    maxIntraClusterDistance = 0;
    for i = 1:nClusters
        clusterIDistance = pdist(X(idx==uniqueClusters(i),:), 'euclidean');
        maxIntraClusterDistance = max(maxIntraClusterDistance, max(clusterIDistance));
    end
    
    % Calculate Dunn index
    dunnIndex = minInterClusterDistance / maxIntraClusterDistance;
end