edu.cmu.tetrad.study.examples.conditions.ExampleCompareFromFiles Maven / Gradle / Ivy
///////////////////////////////////////////////////////////////////////////////
// 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, 2022 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.study.examples.conditions;
import edu.cmu.tetrad.algcomparison.Comparison;
import edu.cmu.tetrad.algcomparison.algorithm.Algorithms;
import edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.Gfci;
import edu.cmu.tetrad.algcomparison.independence.FisherZ;
import edu.cmu.tetrad.algcomparison.score.SemBicScore;
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
*
* new Comparison().saveDataSetAndGraphs("comparison/save1", simulation, parameters);
*
* saves them. For other formats, specialty data loaders can be written to implement the Simulation interface.
*
* @author josephramsey
*/
public class ExampleCompareFromFiles {
public static void main(String... args) {
Parameters parameters = new Parameters();
parameters.set("numRuns", 1);
// parameters.set("numMeasures", 20,100,1000);
parameters.set("numMeasures", 1000);
parameters.set("numLatents", 200);
parameters.set("avgDegree", 2);
parameters.set("sampleSize", 1000);
parameters.set("penaltyDisount", 2);
parameters.set("alpha", 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 MathewsCorrArrow());
statistics.add(new F1Adj());
statistics.add(new F1Arrow());
statistics.add(new StructuralHammingDistance());
statistics.add(new ElapsedCpuTime());
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 Gfci(new FisherZ(), new SemBicScore()));
// algorithms.add(new Fges(new BdeuScore(),true));
// algorithms.add(new Fges(new DiscreteBicScore(),true));
// algorithms.add(new Fges(new SemBicScore()));
// algorithms.add(new Gfci(new ChiSquare(), new DiscreteBicScore())));
Comparison comparison = new Comparison();
comparison.setShowAlgorithmIndices(true);
comparison.setShowSimulationIndices(false);
comparison.setSortByUtility(true);
comparison.setShowUtilities(true);
comparison.setSaveGraphs(true);
//DagToPag p = new DagToPag(graph);
comparison.compareFromFiles("comparison", algorithms, statistics, parameters);
}
}