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.cmu.tetrad.algcomparison.examples;
  
  import edu.cmu.tetrad.algcomparison.Comparison;
  import edu.cmu.tetrad.algcomparison.algorithm.Algorithms;
  import edu.cmu.tetrad.algcomparison.algorithm.mixed.Mgm;
  import edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.*;
  import edu.cmu.tetrad.algcomparison.independence.ConditionalGaussianLRT;
  import edu.cmu.tetrad.algcomparison.independence.FisherZ;
  //import edu.cmu.tetrad.algcomparison.independence.MNLRLRT;
  import edu.cmu.tetrad.algcomparison.independence.MNLRLRT;
  import edu.cmu.tetrad.algcomparison.independence.MVPLRT;
  import edu.cmu.tetrad.algcomparison.score.*;
  import edu.cmu.tetrad.algcomparison.statistic.*;
  import edu.cmu.tetrad.util.Parameters;
  
  /**
   * An example script to load in data sets and graphs from files and analyze them. The
   * files loaded must be in the same format as
   * </p>
   * new Comparison().saveDataSetAndGraphs("comparison/save1", simulation, parameters);
   * </p>
   * saves them. For other formats, specialty data loaders can be written to implement the
   * Simulation interface.
   *
   * @author jdramsey
   */
  public class CompareFromFiles {
      public static void main(String... args) {
          Parameters parameters = new Parameters();
  
          // Can leave the simulation parameters out since
          // we're loading from file here.
  
          parameters.set("numRuns", 3);
          parameters.set("maxDistinctValuesDiscrete", 5);
  
          parameters.set("structurePrior", -0.5);
          parameters.set("fDegree", -1);
          parameters.set("discretize", 0);
  
          parameters.set("alpha", 1e-3, 1e-4);
  
          Statistics statistics = new Statistics();
  
          statistics.add(new ParameterColumn("avgDegree"));
          statistics.add(new ParameterColumn("sampleSize"));
          statistics.add(new AdjacencyPrecision());
          statistics.add(new AdjacencyRecall());
          statistics.add(new ArrowheadPrecision());
          statistics.add(new ArrowheadRecall());
          statistics.add(new ElapsedTime());
  
          statistics.setWeight("AP", 1.0);
          statistics.setWeight("AR", 0.5);
          statistics.setWeight("AHP", 1.0);
          statistics.setWeight("AHR", 0.5);
  
          Algorithms algorithms = new Algorithms();
  
  //        algorithms.add(new Fges(new ConditionalGaussianBicScore()));
  //        algorithms.add(new Fges(new ConditionalGaussianOtherBicScore()));
          algorithms.add(new Fges(new MVPBicScore()));
  //        algorithms.add(new Fges(new MNLRBicScore()));
  //        algorithms.add(new Fges(new DiscreteMixedBicScore()));
  //        algorithms.add(new Cpc(new ConditionalGaussianLRT()));
  //        algorithms.add(new Cpc(new MVPLRT()));
  //        algorithms.add(new Cpc(new MNLRLRT(), new Mgm()));
  
          Comparison comparison = new Comparison();
          comparison.setShowAlgorithmIndices(true);
          comparison.setShowSimulationIndices(true);
          comparison.setSortByUtility(false);
          comparison.setShowUtilities(false);
          comparison.setComparisonGraph(Comparison.ComparisonGraph.true_DAG);
  
          comparison.compareFromFiles("comparison", algorithms, statistics, parameters);
      }
  }
  
  
  
  
  