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The Statistics Toolbox implements the gap statistic as a class in the package `clustering.evaluation` since R2013b: http://www.mathworks.com/help/stats/clustering.evaluation.gapevaluationclass.html
load fisheriris; rng('default'); % For reproducibility eva = evalclusters(meas,'kmeans','gap','KList',[1:6]) figure; plot(eva);
You can also use this file exchange: http://www.mathworks.com/matlabcentral/fileexchange/37905-gap-statistics
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