% Network Analysis Code Readme Author: Yen-Nan Lin
0001 %% Network Analysis Code Readme 0002 % Author: Yen-Nan Lin 0003 0004 %% About 0005 % The code was written and tested in MATLAB R2012a. Goal of this package was to 0006 % analyse the difference between neural networks and theoretical networks in 0007 % horizontal and vertical propagations. Because some functions used random 0008 % number generator (most of the functions are module-related), the scripts might 0009 % generate slightly differnet result in different computers. More details were 0010 % shown in the manuscript. 0011 % 0012 % This package include several toolboxes to analyze networks and plot figures. 0013 % The toolboxes are under in the Toolbox folder. 0014 % 0015 % *Network analysis toolbox* 0016 % 0017 % * 2011-03-27_BCT http://sites.google.com/site/bctnet 0018 % 0019 % *Plotting toolboxes* 0020 % 0021 % * xticklabel_rotate http://www.mathworks.com/matlabcentral/fileexchange/3486-xticklabelrotate 0022 % * ploterr http://www.mathworks.com/matlabcentral/fileexchange/22216-ploterr 0023 % * panel_2.4 http://www.mathworks.com/matlabcentral/fileexchange/20003-panel 0024 % * breakYAxis http://www.mathworks.co.uk/matlabcentral/fileexchange/22378-break-y-axis 0025 % 0026 0027 %% Run 0028 % 0029 % The codes could be classified into 2 groups: scripts and functions. 0030 % All goXXXXXXX.m files should be scripts. Below is a process of standard 0031 % analysis. The step of plotting are not included in the standard analysis process. 0032 % 0033 % # load neural network 0034 % # analyse neural network 0035 % # create theoretical networks based on the loaded neural network 0036 % # analyse theoretical networks 0037 % # compute the average of realisation results 0038 % # plot the result 0039 % 0040 % Here is a standard analysis example. In the matlab, and command 0041 % 0042 % goAnalysis 0043 % 0044 % Then, run specific plotting script based on which figure you want to plot. 0045 % 0046 % If you want to plot result of figure 9, you should run another analysis 0047 % script. However, this scripts may take several hours to compute. 0048 % 0049 % goAnalysisRecur 0050 0051 %% Script of plotting figures 0052 % * fig3.tif = goPlotChConnectMat.m 0053 % * fig4.tif = goPlotHorzDistr.m 0054 % * fig5a.tif = goPlotVert.m 0055 % * fig5b.tif = goPlotHorz.m 0056 % * fig5c.tif = goPlotSummary.m 0057 % * fig6.tif = goPlotChConnectMatIO.m 0058 % * fig7a.tif = goPlotVertIO.m 0059 % * fig7b.tif = goPlotHorzIO.m 0060 % * fig7c.tif = goPlotSummaryIO.m 0061 % * fig8a.tif = goPlotSwAddHub.m 0062 % * fig8b.tif = goPlotRemoveHub.m 0063 % * fig8c.tif = goPlotRemoveHub.m 0064 % * fig8d.tif = goPlotRemoveHub.m 0065 % * fig9a.tif = goPlotRecur.m 0066 % * fig9b.tif = goPlotNewNode.m 0067 % * fig9c.tif = goPlotNPath.m 0068 % * fig11.tif = goPlotChConnectCE.m 0069 0070 0071 %% More information 0072 % 0073 % The full documents of functions and scripts are shown in 0074 % <doc/index.html>. 0075 % 0076 % The dependencies of functions are shown in 0077 % <doc/NA/graph.html>.