edu.cmu.tetrad.study.examples.conditions.Condition2 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.external.*;
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 Condition2 {
public static void main(String... args) {
new Condition2().compileTable();
}
public void generateTetradResults() {
Parameters parameters = new Parameters();
parameters.set("alpha", 0.01);
parameters.set("numRuns", 10);
// parameters.set("penaltyDiscount", 4);
parameters.set("useMaxPOrientationHeuristic", false);
// parameters.set("maxPOrientationMaxPathLength", 3);
Statistics statistics = new Statistics();
statistics.add(new ParameterColumn("numMeasures"));
statistics.add(new ParameterColumn("avgDegree"));
statistics.add(new ParameterColumn("sampleSize"));
statistics.add(new ParameterColumn("faithfulnessAssumed"));
statistics.add(new AdjacencyPrecision());
statistics.add(new AdjacencyRecall());
statistics.add(new ArrowheadPrecision());
statistics.add(new ArrowheadRecall());
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();
Comparison comparison = new Comparison();
comparison.setShowAlgorithmIndices(true);
comparison.setShowSimulationIndices(true);
comparison.setSortByUtility(false);
comparison.setShowUtilities(true);
comparison.setSaveGraphs(true);
comparison.compareFromFiles("/Users/user/comparison-data/condition_2",
"/Users/user/causal-comparisons/condition_2",
algorithms, statistics, parameters);
}
public void compileTable() {
Parameters parameters = new Parameters();
parameters.set("numRuns", 10);
Statistics statistics = new Statistics();
statistics.add(new ParameterColumn("numMeasures"));
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 MathewsCorrAdj());
statistics.add(new MathewsCorrArrow());
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 ExternalAlgorithmTetrad("PC_(\"Peter_and_Clark\"),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmTetrad("PC_(\"Peter_and_Clark\"),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmTetrad("PC-Stable_(\"Peter_and_Clark\"_Stable),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmTetrad("PC-Stable_(\"Peter_and_Clark\"_Stable),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmTetrad("PC-Stable-Max_(\"Peter_and_Clark\"),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmTetrad("PC-Stable-Max_(\"Peter_and_Clark\"),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmTetrad("CPC_(Conservative_\"Peter_and_Clark\"),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmTetrad("CPC_(Conservative_\"Peter_and_Clark\"),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmTetrad("CPC-Stable_(Conservative_\"Peter_and_Clark\"_Stable),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmTetrad("CPC-Stable_(Conservative_\"Peter_and_Clark\"_Stable),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.001"));
//
algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Fisher_Z_Score,_alpha_=_0.001,_faithfulnessAssumed_=_false"));
algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Fisher_Z_Score,_alpha_=_1.0E-4,_faithfulnessAssumed_=_false"));
algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Fisher_Z_Score,_alpha_=_1.0E-8,_faithfulnessAssumed_=_false"));
algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Sem_BIC_Score,_penaltyDiscount_=_2,_faithfulnessAssumed_=_false"));
algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Sem_BIC_Score,_penaltyDiscount_=_4,_faithfulnessAssumed_=_false"));
algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Fisher_Z_Score,_alpha_=_0.001,_faithfulnessAssumed_=_true"));
algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Fisher_Z_Score,_alpha_=_1.0E-4,_faithfulnessAssumed_=_true"));
algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Fisher_Z_Score,_alpha_=_1.0E-8,_faithfulnessAssumed_=_true"));
algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Sem_BIC_Score,_penaltyDiscount_=_2,_faithfulnessAssumed_=_true"));
algorithms.add(new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Sem_BIC_Score,_penaltyDiscount_=_4,_faithfulnessAssumed_=_true"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("MMPC_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("MMPC_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("GrowShrink alpha = 0.01"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("GrowShrink alpha = 0.001"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("IAMB_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("IAMB_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("Fast.IAMB_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("Fast.IAMB_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("Inter.IAMB_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("Inter.IAMB_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("si.hiton.pc_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("si.hiton.pc_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmBnlearnMmhc("MMHC"));
algorithms.add(new ExternalAlgorithmPcalgPc("PC_pcalg_defaults_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmPcalgPc("PC_pcalg_defaults_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmPcalgPc("PC-Stable_pcalg_ncores=4_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmPcalgPc("PC-Stable_pcalg_ncores=4_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmPcalgPc("CPC_pcalg_defaults_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmPcalgPc("CPC_pcalg_defaults_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmPcalgPc("CPC_pcalg_majority.rule_defaults_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmPcalgPc("CPC_pcalg_majority.rule_defaults_alpha_=_0.001"));
algorithms.add(new ExternalAlgorithmPcalgGes("GES_pcalg_defaults_2*log(nrow(data)"));
algorithms.add(new ExternalAlgorithmPcalgGes("GES_pcalg_defaults_4*log(nrow(data)"));
algorithms.add(new ExternalAlgorithmBNTPc("learn.struct.pdag.pc_bnt_alpha_=_0.01"));
algorithms.add(new ExternalAlgorithmBNTPc("learn.struct.pdag.pc_bnt_alpha_=_0.001"));
Comparison comparison = new Comparison();
comparison.setShowAlgorithmIndices(true);
comparison.setShowSimulationIndices(true);
comparison.setSortByUtility(false);
comparison.setShowUtilities(false);
comparison.setSaveGraphs(true);
comparison.setComparisonGraph(Comparison.ComparisonGraph.true_DAG);
comparison.generateReportFromExternalAlgorithms("/Users/user/comparison-data/condition_2",
"/Users/user/causal-comparisons/condition_2", "Comparison.txt",
algorithms, statistics, parameters);
Statistics statistics2 = new Statistics();
statistics2.add(new ParameterColumn("numMeasures"));
statistics2.add(new ParameterColumn("avgDegree"));
statistics2.add(new ParameterColumn("sampleSize"));
statistics2.add(new AdjacencyFp());
statistics2.add(new AdjacencyFn());
statistics2.add(new AdjacencyTp());
statistics2.add(new AdjacencyTn());
statistics2.add(new ArrowheadFp());
statistics2.add(new ArrowheadFn());
statistics2.add(new ArrowheadTp());
statistics2.add(new ArrowheadTn());
statistics2.add(new ElapsedCpuTime());
//
comparison.generateReportFromExternalAlgorithms("/Users/user/comparison-data/condition_2",
"/Users/user/causal-comparisons/condition_2", "Counts.txt",
algorithms, statistics2, parameters);
}
}