Version 0.1 
Authors: Kranti Konganti, Wang G, Yang E and James J. Cai 
(C) Texas A&M University. 
 
$LastChangedDate: 2012-07-28 13:52:41 -0500 (Sat, 28 Jul 2012) $ 
$LastChangedRevision: 254 $ 
$LastChangedBy: jcai $ 
 
 
==== SBEToolbox Functions ==== 
 
 
  Generate Random Networks 
  ------------------------ 
 
      randnet_er               - Generate a random Erdös-Réyni network. 
      randnet_rl               - Generate a random Ring Lattice network. 
      randnet_sw               - Generate a random Small world network. 
 
  Graph Statistics 
  ---------------- 
 
      graph_clustercoeff       - Calculate overall clustering coefficient of the graph. 
      graph_diameter           - Calculate diameter of the graph. 
      graph_efficiency         - Calculate efficiency measure of the graph. 
      graph_meandist           - Calculate mean distance of the graph. 
      graph_density            - Calculate density of the graph. 
 
  Node Statistics 
  --------------- 
 
      bridging_centrality      - Calculate Bridging Centrality. 
      closeness_centrality     - Calculate Closeness Centrality. 
      eccentricity_centrality  - Calculate Eccentricity Centrality. 
      delta_centrality         - Calculate Delta Centrality. 
      current_info_flow        - Calculate Current Information Flow. 
      assortativitycoeff       - Calculate Assortativity Coefficient. 
      bridgingcoeff            - Calculate Bridging Coefficient. 
      brokeringcoeff           - Calculate Brokering Coefficient. 
      clusteringcoeff          - Calculate Clustering Coefficient. 
      soffercc                 - Calculate Clustering Coefficient of Soffer & Vázquez (2005). 
      order2cc                 - Calculate Clustering Coefficient considering 2nd level of connections. 
      hierarchy                - Calculate Degree of hierarchy. 
      kclique                  - Caldulate K-clique. 
      kcore                    - Calculate K-core of network. 
      locavgcon                - Calculate Local Average Connectivity. 
      neighborhood_conn        - Calculate Neighborhood Connectivity. 
      participationcoeff       - Calculate Participation Coefficient. 
      richclubcoeff            - Calculate Rich Club Coefficient. 
      smallworldindex          - Calculate Small World Index. 
      within_module_deg        - Calculate Within Module Degree. 
 
  Module Detection 
  ---------------- 
 
      clusteronerun            - Detect modeules using ClusterONE algorithm. 
      mcode                    - Detect modeules using mcode algorithm. 
      mcl                      - Implementation of Stijn van Dongen's algorithm to deduce clusters of current graph. 
 
  Input & Output 
  -------------- 
 
      readmat2sbe              - Read network information in MATLAB matrix format into G. 
      readpajek2sbe            - Read network information PAJEK format into G. 
      readsif2sbe              - Read network information in SIF format into G. 
      readtab2sbe              - Read network information on TAB format into G. 
      writeadjmat2mat          - Write adjacency matrix into MAT file. 
      writeattribute2tab       - Write node attribute in a TAB delimited file. 
      writesbe2mat             - Write Network information as MATLAB MAT file. 
      writesbe2pajek           - Write network information in PAJEK format. 
      writesbe2protovis        - Write network information into Protovis accepted format. 
      writesbe2sif             - Write network information in SIF format. 
      writesbe2tab             - Write network information in TAB Delimited format. 
      writesbe2xml             - Write network information into XML format for visualization plugins. 
 
  Visualization 
  ------------- 
 
      plotnet                  - View network in a plot. 
      plotnet_edgewidth        - View network in a plot with defined edge width. 
      plotnet_curve            - View network in a plot with curved edges. 
      plotnet_treering         - View network in a treering plot. 
      viewnetsvg               - View network using SVG. 
      powerlawplot             - Plot relationship between degree and number of nodes. 
      sbe_layout               - Gateway function for layout methods. 
 
  Miscellanous 
  ------------ 
 
      laplacian                - Get graph laplacian matrix. 
      incidence                - Conversion from adjacency matrix to incidence matrix. 
      modmat                   - Modularity matrix for undirected graph. 
      symmetrizeadjmat         - Symmetrize network G. 
      issimple                 - Check if network is simple (no self-loops, no double edges). 
      issymmetric              - Check if network loaded into G is symmetric. 
      cytoscaperun             - Export network in SIF format and invoke external program Cytoscape. 
      moduleid2net             - Represents module id output in a matrix for plotting