% 
% example epage ???104 
% problem epage 129 
% 
% 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'); addpath( '../../Code/eda_toolbox' ); 

% Modified from Example 5.5: which shows the graphical Mojena rule.

set(0,'recursionlimit',1000); 

%X = load_spam(1,0,1,0);   % <- preprocess using the z-score ... only
%X = load_spam(0,0,0,1);   % <- do PCA based dimensionality reduction on the direct data ... 
%X = load_spam(1,0,1,1);   % <- do PCA based dimensionality reduction ... with z-score ... produces chaining in the dendrogram
%X = load_spam(1,0,1,2);  % <- do SVD based dimensionality reduction ... with z-score ... produces chaining in the dendrogram 
X = load_spam(1,1,1,1);  % <- do PCA based dimensionality reduction ... with z-score ... seems to work 
%X = load_spam(1,1,1,2);  % <- do SVD based dimensionality reduction (with column ordering) ... with z-score ... 
[n,p] = size(X);

y = pdist(X,'euclidean'); 

dn = '../../WriteUp/Graphics/Chapter5/';
%dn = '../Graphics/Chapter5/';

linkage_type = 'average'; 
%linkage_type = 'complete'; 

% We will do this somewhat differently, so it is in keeping with the types of 'elbow' plots in previous
% chapters and applcations. 

% Get the distances and the linkage.
% Use the standardized Euclidean distance.
Y = pdist(X,'euclidean');
Z = linkage(Y,'average');
% Plot dendrogram with fewer leaf nodes.
dendrogram(Z,15);

nc = 10;
% Flip the Z matrix - makes it easier.
Zf = flipud(Z);
% Now get the vector of means
% and standard deviations
for i = 1:nc
    abar(i) = mean(Zf(i:end,3));
    astd(i) = std(Zf(i:end,3));
end
% Get the y values for plotting.
yv = (Zf(1:nc,3) - abar(:))./astd(:);
xv = 1:nc;
figure; plot(xv,yv,'-o')
xlabel('Number of Clusters')
ylabel('Standardized Fusion Levels')
saveas( gcf, '../../WriteUp/Graphics/Chapter5/prob_5_11_spam_mojena_1', 'epsc' ); 

% We can also plot just the fusion levels
% and look for the elbow.
figure; plot(1:nc,Zf(1:nc,3),'o-')
xlabel('Number of Clusters')
ylabel('Raw Fusion Levels')
saveas( gcf, '../../WriteUp/Graphics/Chapter5/prob_5_11_spam_mojena_2', 'epsc' );