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tetrad-lib/src/test/java/edu/cmu/tetrad/test/TestConditionalGaussianSimulation.java
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| /////////////////////////////////////////////////////////////////////////////// | ||
| // 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 // | ||
| /////////////////////////////////////////////////////////////////////////////// | ||
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| package edu.cmu.tetrad.test; | ||
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| import edu.cmu.tetrad.algcomparison.Comparison; | ||
| import edu.cmu.tetrad.algcomparison.algorithm.Algorithms; | ||
| import edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.*; | ||
| import edu.cmu.tetrad.algcomparison.graph.RandomForward; | ||
| import edu.cmu.tetrad.algcomparison.score.ConditionalGaussianBicScore; | ||
| import edu.cmu.tetrad.algcomparison.simulation.*; | ||
| import edu.cmu.tetrad.algcomparison.statistic.*; | ||
| import edu.cmu.tetrad.util.Parameters; | ||
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| /** | ||
| * An example script to simulate data and run a comparison analysis on it. | ||
| * | ||
| * @author jdramsey | ||
| */ | ||
| public class TestConditionalGaussianSimulation { | ||
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| public void test1() { | ||
| Parameters parameters = new Parameters(); | ||
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| parameters.set("numRuns", 1); | ||
| parameters.set("numMeasures", 100); | ||
| parameters.set("avgDegree", 4); | ||
| parameters.set("sampleSize", 1000); | ||
| parameters.set("penaltyDiscount", 2); | ||
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| parameters.set("maxDegree", 8); | ||
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| parameters.set("numCategories", 2, 3, 4, 5); | ||
| parameters.set("percentDiscrete", 50); | ||
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| parameters.set("assumeMixed", false); | ||
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| parameters.set("intervalBetweenRecordings", 20); | ||
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| parameters.set("varLow", 1.); | ||
| parameters.set("varHigh", 3.); | ||
| parameters.set("coefLow", .5); | ||
| parameters.set("coefHigh", 1.5); | ||
| parameters.set("coefSymmetric", true); | ||
| parameters.set("meanLow", -1); | ||
| parameters.set("meanHigh", 1); | ||
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| Statistics statistics = new Statistics(); | ||
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| statistics.add(new ParameterColumn("numCategories")); | ||
| statistics.add(new ParameterColumn("assumeMixed")); | ||
| statistics.add(new AdjacencyPrecision()); | ||
| statistics.add(new AdjacencyRecall()); | ||
| statistics.add(new ArrowheadPrecision()); | ||
| statistics.add(new ArrowheadRecall()); | ||
| statistics.add(new ElapsedTime()); | ||
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| statistics.setWeight("AP", 1.0); | ||
| statistics.setWeight("AR", 0.5); | ||
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| Algorithms algorithms = new Algorithms(); | ||
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| algorithms.add(new Fges(new ConditionalGaussianBicScore())); | ||
| // algorithms.add(new PcMax(new ConditionalGaussianLRT())); | ||
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| Simulations simulations = new Simulations(); | ||
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| simulations.add(new ConditionalGaussianSimulation(new RandomForward())); | ||
| // simulations.add(new LeeHastieSimulation(new RandomForward())); | ||
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| Comparison comparison = new Comparison(); | ||
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| comparison.setShowAlgorithmIndices(true); | ||
| comparison.setShowSimulationIndices(false); | ||
| comparison.setSortByUtility(false); | ||
| comparison.setShowUtilities(false); | ||
| comparison.setParallelized(false); | ||
| comparison.setSaveGraphs(true); | ||
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| comparison.setTabDelimitedTables(true); | ||
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| comparison.compareFromSimulations("comparison", simulations, algorithms, statistics, parameters); | ||
| } | ||
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| public static void main(String...args) { | ||
| new TestConditionalGaussianSimulation().test1(); | ||
| } | ||
| } | ||
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tetrad-lib/src/test/java/edu/cmu/tetrad/test/TestConditionalLikelihood.java
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