code: ///////////////////////////////////////////////////////////////////////////////
  // For information as to what this class does, see the Javadoc, below.       //
  // Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006,       //
  // 2007, 2008, 2009, 2010, 2014, 2015 by Peter Spirtes, Richard Scheines, Joseph   //
  // Ramsey, and Clark Glymour.                                                //
  //                                                                           //
  // This program is free software; you can redistribute it and/or modify      //
  // it under the terms of the GNU General Public License as published by      //
  // the Free Software Foundation; either version 2 of the License, or         //
  // (at your option) any later version.                                       //
  //                                                                           //
  // This program is distributed in the hope that it will be useful,           //
  // but WITHOUT ANY WARRANTY; without even the implied warranty of            //
  // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the             //
  // GNU General Public License for more details.                              //
  //                                                                           //
  // You should have received a copy of the GNU General Public License         //
  // along with this program; if not, write to the Free Software               //
  // Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA //
  ///////////////////////////////////////////////////////////////////////////////
  
  package edu.pitt.csb.mgm;
  
  import edu.cmu.tetrad.data.DataSet;
  import edu.cmu.tetrad.graph.Graph;
  import edu.cmu.tetrad.graph.GraphUtils;
  import edu.cmu.tetrad.search.IndTestMultinomialLogisticRegression;
  import edu.cmu.tetrad.search.PcStable;
  import edu.cmu.tetrad.search.SearchGraphUtils;
  
  import java.io.File;
  
  /**
   * Created by ajsedgewick on 9/10/15.
   */
  public class ExploreIndepTests {
      public static void main(String[] args){
  //        Graph g = new EdgeListGraph();
  //        g.addNode(new ContinuousVariable("X1"));
  //        g.addNode(new ContinuousVariable("X2"));
  //        g.addNode(new DiscreteVariable("X3", 4));
  //        g.addNode(new DiscreteVariable("X4", 4));
  //        g.addNode(new ContinuousVariable("X5"));
  //
  //        g.addDirectedEdge(g.getNode("X1"), g.getNode("X2"));
  //        g.addDirectedEdge(g.getNode("X2"), g.getNode("X3"));
  //        g.addDirectedEdge(g.getNode("X3"), g.getNode("X4"));
  //        g.addDirectedEdge(g.getNode("X4"), g.getNode("X5"));
  //
  //        GeneralizedSemPm pm = MixedUtils.GaussianCategoricalPm(g, "Split(-1.5,-.5,.5,1.5)");
  ////        System.out.println(pm);
  //
  //        GeneralizedSemIm im = MixedUtils.GaussianCategoricalIm(pm);
  ////        System.out.println(im);
  //
  //        int samps = 200;
  //        DataSet ds = im.simulateDataAvoidInfinity(samps, false);
  //        ds = MixedUtils.makeMixedData(ds, MixedUtils.getNodeDists(g));
  //        //System.out.println(ds);
  //        System.out.println(ds.isMixed());
          try {
              String path = ExampleMixedSearch.class.getResource("test_data").getPath();
              Graph trueGraph = SearchGraphUtils.patternFromDag(GraphUtils.loadGraphTxt(new File(path, "DAG_0_graph.txt")));
              DataSet ds = MixedUtils.loadDataSet(path, "DAG_0_data.txt");
  
              IndTestMultinomialLogisticRegression indMix = new IndTestMultinomialLogisticRegression(ds, .05);
              IndTestMultinomialLogisticRegressionWald indWalLin = new IndTestMultinomialLogisticRegressionWald(ds, .05, true);
              IndTestMultinomialLogisticRegressionWald indWalLog = new IndTestMultinomialLogisticRegressionWald(ds, .05, false);
  
              PcStable s1 = new PcStable(indMix);
              PcStable s2 = new PcStable(indWalLin);
              PcStable s3 = new PcStable(indWalLog);
  
              long time = System.currentTimeMillis();
              Graph g1 = SearchGraphUtils.patternFromDag(s1.search());
              System.out.println("Mix Time " + ((System.currentTimeMillis() - time)/1000.0));
  
               time = System.currentTimeMillis();
              Graph g2 = SearchGraphUtils.patternFromDag(s2.search());
              System.out.println("Wald lin Time " + ((System.currentTimeMillis() - time)/1000.0));
  
               time = System.currentTimeMillis();
              Graph g3 = SearchGraphUtils.patternFromDag(s3.search());
              System.out.println("Wald log Time " + ((System.currentTimeMillis() - time)/1000.0));
  
  //            System.out.println(g);
  //            System.out.println("IndMix: " + s1.search());
  //            System.out.println("IndWalLin: " + s2.search());
  //            System.out.println("IndWalLog: " + s3.search());
  
              System.out.println(MixedUtils.EdgeStatHeader);
              System.out.println(MixedUtils.stringFrom2dArray(MixedUtils.allEdgeStats( trueGraph, g1)));
              System.out.println(MixedUtils.stringFrom2dArray(MixedUtils.allEdgeStats( trueGraph, g2)));
              System.out.println(MixedUtils.stringFrom2dArray(MixedUtils.allEdgeStats( trueGraph, g3)));
          } catch (Throwable t){
              t.printStackTrace();
          }
      }
  
  }
  
  