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.oracle.pag.TsFci;
  import edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.TsGfci;
  import edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.TsImages;
  import edu.cmu.tetrad.algcomparison.graph.RandomForward;
  import edu.cmu.tetrad.algcomparison.independence.FisherZ;
  import edu.cmu.tetrad.algcomparison.score.SemBicScore;
  import edu.cmu.tetrad.search.IndTestScore;
  import edu.cmu.tetrad.search.IndependenceTest;
  import edu.cmu.tetrad.search.Score;
  import edu.cmu.tetrad.search.ScoredIndTest;
  import edu.cmu.tetrad.util.Parameters;
  import edu.cmu.tetrad.algcomparison.simulation.Simulations;
  import edu.cmu.tetrad.algcomparison.simulation.TimeSeriesSemSimulation;
  import edu.cmu.tetrad.algcomparison.statistic.*;
  
  /**
   * An example script to simulate time series data and run a comparison analysis on it.
   *
   * @authors jdramsey, dmalinsky
   */
  public class ExampleCompareSimulationTimeSeries {
      public static void main(String... args) {
          Parameters parameters = new Parameters();
  
          parameters.set("numRuns", 10);
          parameters.set("numMeasures", 10);
          parameters.set("avgDegree", 4);
          parameters.set("sampleSize", 500);
          parameters.set("alpha", 1e-4, 1e-3, 1e-2);
  
          Statistics statistics = new Statistics();
  
          statistics.add(new AdjacencyPrecision());
          statistics.add(new AdjacencyRecall());
          statistics.add(new ArrowheadPrecision());
          statistics.add(new ArrowheadRecall());
          statistics.add(new MathewsCorrAdj());
          statistics.add(new MathewsCorrArrow());
          statistics.add(new F1Adj());
          statistics.add(new F1Arrow());
          statistics.add(new SHD());
          statistics.add(new ElapsedTime());
  
          statistics.setWeight("AP", 1.0);
          statistics.setWeight("AR", 0.5);
  
          Algorithms algorithms = new Algorithms();
  
          algorithms.add(new TsFci(new FisherZ()));
          algorithms.add(new TsGfci(new FisherZ(), new SemBicScore()));
          algorithms.add(new TsImages(new SemBicScore()));
  
          Simulations simulations = new Simulations();
  
          simulations.add(new TimeSeriesSemSimulation(new RandomForward()));
  
          Comparison comparison = new Comparison();
  
          comparison.setSortByUtility(true);
          comparison.setShowUtilities(true);
  
          comparison.compareFromSimulations("comparison", simulations, algorithms, statistics, parameters);
      }
  }
  
  
  
  
  