% 
% 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.

X = load_geyser(0,0);
%X = load_geyser(1,1); % the z-score no difference in the clusters ... 
[n,p] = size(X);

% 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);

% the code below is basically a call to: 
%nc = 10; 
%mojenaplot(Z,nc); 

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_geyser_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_geyser_mojena_2', 'epsc' );