% 
% example epage 104 
% problem epage 128 
% 
% Written by:
% -- 
% John L. Weatherwax                2005-08-14
% 
% email: wax@alum.mit.edu
% 
% Please send comments and especially bug reports to the
% above email address.
% 
%-----

close all; drawnow; 
clc; 
clear; addpath( '../../Code/eda_data' ); addpath('../Chapter1'); 

% get the iris data without any processing: 
% 
[data,vars,classes] = load_iris(0,0,0); 

y = pdist(data,'euclidean'); 

z = linkage(y); % <- use the default of single linkage d(S,R) = min_{i \in S,j \in R}(x_i,x_j) 
figure; dendrogram(z); 
title( 'single linkage' ); 
saveas( gcf, '../../WriteUp/Graphics/Chapter5/prob_5_1_iris_den_sl', 'epsc' ); 

% try with the centroid clustering:
% 
z = linkage(y,'centroid'); 
figure; dendrogram(z); 
title( 'centroid linkage' ); 
saveas( gcf, '../../WriteUp/Graphics/Chapter5/prob_5_1_iris_den_cent', 'epsc' ); 

% try with the mahalanobis distance:
% 
y = pdist(data,'mahalanobis'); 
z = linkage(y,'centroid'); 
figure; dendrogram(z); 
title( 'centroid linkage (Mahalanobis distance)' ); 
saveas( gcf, '../../WriteUp/Graphics/Chapter5/prob_5_1_iris_den_cent_mah', 'epsc' ); 


% try the average distance ... considered by many to be quite good: 
% 
y = pdist(data,'euclidean'); 
z = linkage(y,'average'); 
figure; dendrogram(z); 
title( 'dendrogram for the iris dataset: average linkage' ); 
%saveas( gcf, '../../WriteUp/Graphics/Chapter5/prob_5_1_iris_den_average', 'epsc' );