updated references

bug in mean clustering coefficient

crqa.m

@@ -121,22 +121,18 @@ function xout=crqa(varargin)
 %    See also CRQAD, CRQAD_BIG, CRP, CRP2, CRP_BIG, DL, TT, PSS.
 %
 %    References: 
-%    Trulla, L. L., Giuliani, A., Zbilut, J. P., Webber Jr., C. L.: 
-%    Recurrence quantification analysis of the logistic equation with 
-%    transients, Phys. Lett. A, 223, 1996.
-%
-%    Marwan, N., Wessel, N., Meyerfeldt, U., Schirdewan, A., Kurths, J.: 
-%    Recurrence Plot Based Measures of Complexity and its Application to 
-%    Heart Rate Variability Data, Phys. Rev. E, 66(2), 2002.
-%
-%    Gao, J. B.: 
-%    Recurrence Time Statistics for Chaotic Systems and Their 
-%    Applications, Phys. Rev. Lett., 83(16), 1999.
+%    Marwan, N., Romano, M. C., Thiel, M., Kurths, J.: 
+%    Recurrence Plots for the Analysis of Complex Systems, 
+%    Phys. Rep., 438, 2007.
 %
 %    Little, M., McSharry, P., Roberts, S., Costello, D., Moroz, I.:
 %    Exploiting Nonlinear Recurrence and Fractal Scaling Properties 
 %    for Voice Disorder Detection, Biomed. Eng. Online, 6, 2007.
 %
+%    Boccaletti, S., Latora, V., Moreno, Y., Chavez, M., Hwang, D.-U.:
+%    Complex networks: Structures and dynamics,
+%    Phys. Rep., 424, 2006.
+%
 %    Marwan, N., Donges, J. F., Zou, Y., Donner, R. V., Kurths, J.: 
 %    Complex network approach for recurrence analysis of time series, 
 %    Phys. Lett. A, 373(46), 2009. 
@@ -153,6 +149,9 @@ function xout=crqa(varargin)
 % $Revision$
 %
 % $Log$
+% Revision 5.41  2010/06/30 12:01:53  marwan
+% RPDE, Clustering and Transitivity added
+%
 % Revision 5.40  2010/06/29 12:48:56  marwan
 % better debugging performance if error occurs
 %
@@ -299,7 +298,7 @@ splash_gpl('crp');
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% check and read the input
 
-try 
+%try 
 errcode=1;
 
    set(0,'ShowHidden','on')
@@ -765,7 +764,7 @@ case 'init'
   ylabel('TT')
 
   h=axes(props.axes,...
-            'Tag','crqa_axes_T1',...
+            'Tag','crqa_axes_RTE',...
             'Box','On',...
             'Position',[11.2017    axes_base+0*(axes_height+axes_hoffset)   28.1785+15    axes_height]);    
   ylabel('T_1')
@@ -945,7 +944,7 @@ case 'init'
   
   set(0,'ShowHidden','on')
   set(h8, 'HandleVis','CallBack')
-  tags={'crqa_Fig';'axes_logo';'text_logo';'crqa_theiler';'frame';'text';'crqa_axes_Data';'crqa_axes_Var';'crqa_axes_CoVar';'crqa_axes_RR';'crqa_axes_DET';'crqa_axes_L';'crqa_axes_ENTR';'crqa_axes_LAM';'crqa_axes_TT';'crqa_axes_T1';'crqa_axes_T2';'crqa_m';'crqa_maxLag';'crqa_method';'crqa_eps';'crqa_lmin';'crqa_vmin';'crqa_w';'crqa_ws';'crqa_button_store';'crqa_button_print';'crqa_button_close';'crqa_button_apply'};
+  tags={'crqa_Fig';'axes_logo';'text_logo';'crqa_theiler';'frame';'text';'crqa_axes_Data';'crqa_axes_Var';'crqa_axes_CoVar';'crqa_axes_RR';'crqa_axes_DET';'crqa_axes_L';'crqa_axes_ENTR';'crqa_axes_LAM';'crqa_axes_TT';'crqa_axes_RTE';'crqa_axes_T2';'crqa_m';'crqa_maxLag';'crqa_method';'crqa_eps';'crqa_lmin';'crqa_vmin';'crqa_w';'crqa_ws';'crqa_button_store';'crqa_button_print';'crqa_button_close';'crqa_button_apply'};
   h=[];
   for i=1:length(tags); h=[h; findobj('Tag',tags{i})]; end
   set(h,'Units','Norm')
@@ -995,7 +994,7 @@ case 'store'
     h=findobj('Tag','crqa_axes_ENTR','Parent',gcf); h_axes.h(6)=h(1);
     h=findobj('Tag','crqa_axes_LAM','Parent',gcf); h_axes.h(7)=h(1);
     h=findobj('Tag','crqa_axes_TT','Parent',gcf); h_axes.h(8)=h(1);
-    h=findobj('Tag','crqa_axes_T1','Parent',gcf); h_axes.h(9)=h(1);
+    h=findobj('Tag','crqa_axes_RTE','Parent',gcf); h_axes.h(9)=h(1);
     h=findobj('Tag','crqa_axes_T2','Parent',gcf); h_axes.h(10)=h(1);
     h=findobj('Tag','uniLogo');
     tags={'text_logo';'frame';'text';'crqa_m';'crqa_maxLag';'crqa_method';'crqa_eps';'crqa_lmin';'crqa_vmin';'crqa_theiler';'crqa_w';'crqa_ws';'crqa_button_store';'crqa_button_print';'crqa_button_close';'crqa_button_apply';};
@@ -1324,11 +1323,11 @@ for i=1:wstep:Nx-w;
          %% network measures
          % global clustering coefficient
          errcode=279;
-         kv = sum(X,1); % degree of nodes
-         Clust = diag(X*X*X)' ./ (kv .* (kv-1));
+         kv = sum(X_theiler,1); % degree of nodes
+         Clust = mean(diag(X_theiler*X_theiler*X_theiler)' ./ (kv .* (kv-1)));
          % transitivity
-         denom = sum(sum(X * X));
-         Trans = trace(X*X*X)/denom
+         denom = sum(sum(X_theiler * X_theiler));
+         Trans = trace(X_theiler*X_theiler*X_theiler)/denom;
          
      end % end plugin
   
@@ -1412,16 +1411,16 @@ if ~nogui
     set(0,'showhidden','on')
     errcode=30;
     h=findobj('Tag','crqa_Fig'); if ~isempty(h), set(0,'CurrentFigure',h(1)); end
-    tx={'RR';'DET';'L';'ENTR';'LAM';'TT';'T_1';'T_2';'Variance';'Covariance'};
-    index=[1,2,3,5,6,7,9,10,15,16,17];
-    tags={'crqa_axes_RR','crqa_axes_DET','crqa_axes_L','crqa_axes_ENTR','crqa_axes_LAM','crqa_axes_TT','crqa_axes_T1','crqa_axes_T2','crqa_axes_Var','crqa_axes_CoVar'};
+    tx={'RR';'DET';'L';'ENTR';'LAM';'TT';'RTE';'T_2';'Variance';'Covariance'};
+    index=[1,2,3,5,6,7,9,11,15,16,17];
+    tags={'crqa_axes_RR','crqa_axes_DET','crqa_axes_L','crqa_axes_ENTR','crqa_axes_LAM','crqa_axes_TT','crqa_axes_RTE','crqa_axes_T2','crqa_axes_Var','crqa_axes_CoVar'};
     h=findobj('Tag','crqa_axes_RR','Parent',gcf); h_axes.h(1)=h(1);
     h=findobj('Tag','crqa_axes_DET','Parent',gcf); h_axes.h(2)=h(1);
     h=findobj('Tag','crqa_axes_L','Parent',gcf); h_axes.h(3)=h(1);
     h=findobj('Tag','crqa_axes_ENTR','Parent',gcf); h_axes.h(4)=h(1);
     h=findobj('Tag','crqa_axes_LAM','Parent',gcf); h_axes.h(5)=h(1);
     h=findobj('Tag','crqa_axes_TT','Parent',gcf); h_axes.h(6)=h(1);
-    h=findobj('Tag','crqa_axes_T1','Parent',gcf); h_axes.h(7)=h(1);
+    h=findobj('Tag','crqa_axes_RTE','Parent',gcf); h_axes.h(7)=h(1);
     h=findobj('Tag','crqa_axes_T2','Parent',gcf); h_axes.h(8)=h(1);
     h=findobj('Tag','crqa_axes_Var','Parent',gcf); h_axes.h(9)=h(1);
     if ~all(x(:)==y(:)), h=findobj('Tag','crqa_axes_CoVar','Parent',gcf); h_axes.h(10)=h(1); end
@@ -1478,8 +1477,8 @@ end
 
 
 
-%if 0
-catch
+if 0
+%catch
   if nogui~=2, if ishandle(hw), close(hw), end , end
   if nargout, xout = NaN; end