Examples with Parameters edu.cmu.tetrad.util.Parameters used on opensource projects

Example 36 with Parameters

use of edu.cmu.tetrad.util.Parameters in project tetrad by cmu-phil.

the class SessionNode method createModelUsingArguments.

/**
 * Creates model using the given arguments, if possible. If not possible,
 * the field this.model is unchanged.
 */
private void createModelUsingArguments(Class modelClass, List<Object> models) throws Exception {
    if (!(SessionModel.class.isAssignableFrom(modelClass))) {
        throw new ClassCastException("Model class must implement SessionModel: " + modelClass);
    }
    // Try to find a constructor of the model class that exactly
    // matches the types of these models.
    Constructor[] constructors = modelClass.getConstructors();
    for (Constructor constructor : constructors) {
        Class[] constructorTypes = constructor.getParameterTypes();
        Object[] arguments = null;
        if (constructorTypes.length == 2 && constructorTypes[0].isArray() && constructorTypes[1] == Parameters.class) {
            List<Object> _objects = new ArrayList<>();
            Class<?> c1 = constructorTypes[0].getComponentType();
            Parameters parameters = null;
            for (int i = 0; i < models.size(); i++) {
                Class<?> c2 = models.get(i).getClass();
                if ((c1.isAssignableFrom(c2))) {
                    _objects.add(models.get(i));
                }
                if (c2 == Parameters.class) {
                    parameters = (Parameters) models.get(i);
                }
            }
            if (_objects.isEmpty()) {
                return;
            }
            if (parameters != null) {
                Object o = Array.newInstance(c1, _objects.size());
                for (int i = 0; i < _objects.size(); i++) {
                    Array.set(o, i, _objects.get(i));
                }
                arguments = new Object[] { o, parameters };
            } else {
                Object o = Array.newInstance(c1, _objects.size());
                for (int i = 0; i < _objects.size(); i++) {
                    Array.set(o, i, _objects.get(i));
                }
                arguments = new Object[] { o };
            }
        }
        if (arguments == null) {
            arguments = assignParameters(constructorTypes, models);
        }
        if (constructorTypes.length == 0)
            continue;
        if (arguments != null) {
            try {
                this.model = (SessionModel) constructor.newInstance(arguments);
                this.model.setName(getDisplayName());
            } catch (InstantiationException e) {
                e.printStackTrace();
                continue;
            // throw e;
            } catch (IllegalAccessException e) {
                e.printStackTrace();
                continue;
            // throw e;
            } catch (InvocationTargetException e) {
                String packagePath = modelClass.getName();
                int begin = packagePath.lastIndexOf('.') + 1;
                String name = packagePath.substring(begin, packagePath.length());
                if (e.getTargetException() instanceof ThreadDeath) {
                    e.printStackTrace();
                    return;
                }
                e.printStackTrace();
                if (e.getCause().getMessage() != null && !e.getCause().getMessage().isEmpty()) {
                    throw new InvocationTargetException(e, e.getCause().getMessage());
                } else {
                    throw new InvocationTargetException(e, "Could not construct node; root cause: " + e.getCause().getMessage() + " " + packagePath + " " + begin + " " + name);
                }
            }
            this.modelParamTypes = constructorTypes;
            this.lastModelClass = modelClass;
            getSessionSupport().fireModelCreated(this);
            // continue;
            break;
        }
    }
}

Example 37 with Parameters

use of edu.cmu.tetrad.util.Parameters in project tetrad by cmu-phil.

the class Condition1 method generateTetradResults.

public void generateTetradResults() {
    Parameters parameters = new Parameters();
    parameters.set("alpha", 0.001);
    parameters.set("numRuns", 10);
    // parameters.set("penaltyDiscount", 4);
    parameters.set("useMaxPOrientationHeuristic", true);
    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 AdjacencyPrecision());
    statistics.add(new AdjacencyRecall());
    statistics.add(new ArrowheadPrecision());
    statistics.add(new ArrowheadRecall());
    statistics.add(new ElapsedTime());
    // statistics.add(new PercentBidirectedEdges());
    // statistics.add(new NumAmbiguousTriples());
    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 Pc(new FisherZ()));
    // algorithms.add(new PcStable(new FisherZ()));
    // algorithms.add(new PcStableMax(new FisherZ(), false));
    // algorithms.add(new Cpc(new FisherZ()));
    // algorithms.add(new CpcStable(new FisherZ()));
    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_1",
    // "/Users/user/causal-comparisons/condition_1",
    // algorithms, statistics, parameters);
    // 
    // algorithms = new Algorithms();
    // 
    // parameters.set("alpha", 0.001, 0.0001, 1e-8);
    // parameters.set("faithfulnessAssumed", true);
    // //
    // algorithms.add(new Fges(new FisherZScore()));
    // 
    // comparison.compareFromFiles("/Users/user/comparison-data/condition_1",
    // "/Users/user/causal-comparisons/condition_1",
    // algorithms, statistics, parameters);
    // 
    // algorithms = new Algorithms();
    parameters.set("penaltyDiscount", 4);
    // 
    algorithms.add(new Fges(new SemBicScore()));
    comparison.compareFromFiles("/Users/user/comparison-data/condition_1", "/Users/user/causal-comparisons/condition_1", algorithms, statistics, parameters);
}

Example 38 with Parameters

use of edu.cmu.tetrad.util.Parameters in project tetrad by cmu-phil.

the class Condition2 method compileTable.

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 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 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 ExternalAlgorithmBnlearnMmhc("iamb_alpha_=_0.001.test=cor"));
    // algorithms.add(new ExternalAlgorithmBnlearnMmhc("iamb_alpha_=_0.001.test=mc-cor"));
    // algorithms.add(new ExternalAlgorithmBnlearnMmhc("iamb_alpha_=_0.001.test=mc-mi-g"));
    // algorithms.add(new ExternalAlgorithmBnlearnMmhc("iamb_alpha_=_0.001.test=mc-zf"));
    // algorithms.add(new ExternalAlgorithmBnlearnMmhc("iamb_alpha_=_0.001.test=mi-g"));
    // algorithms.add(new ExternalAlgorithmBnlearnMmhc("iamb_alpha_=_0.001.test=mi-g-sh"));
    // algorithms.add(new ExternalAlgorithmBnlearnMmhc("iamb_alpha_=_0.001.test=smc-cor"));
    // algorithms.add(new ExternalAlgorithmBnlearnMmhc("iamb_alpha_=_0.001.test=smc-mi-g"));
    // algorithms.add(new ExternalAlgorithmBnlearnMmhc("iamb_alpha_=_0.001.test=smc-zf"));
    // algorithms.add(new ExternalAlgorithmBnlearnMmhc("iamb_alpha_=_0.001.test=zf"));
    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"));
    // algorithms.add(new ExternalAlgorithmIntersection("Intersection (Tetrad) CPC, PC_Stable-Max, CPC-Stable",
    // new ExternalAlgorithmTetrad("CPC_(Conservative_\"Peter_and_Clark\"),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.001"),
    // new ExternalAlgorithmTetrad("PC-Stable-Max_(\"Peter_and_Clark\"),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.001"),
    // new ExternalAlgorithmTetrad("CPC-Stable_(Conservative_\"Peter_and_Clark\"_Stable),_Priority_Rule,_using_Fisher_Z_test,_alpha_=_0.001")
    // 
    // ));
    // 
    // algorithms.add(new ExternalAlgorithmIntersection("Intersection FGES alpha .001, 1e-8, penalty 2",
    // new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Fisher_Z_Score,_alpha_=_0.001"),
    // new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Fisher_Z_Score,_alpha_=_1.0E-8"),
    // new ExternalAlgorithmTetrad("FGES_(Fast_Greedy_Equivalence_Search)_using_Sem_BIC_Score,_penalty_discount_=_2.0")
    // ));
    // 
    // algorithms.add(new ExternalAlgorithmIntersection("Intersection PC, CPC, CPC majority, pcalg",
    // new ExternalAlgorithmPcalgPc("PC_pcalg_defaults_alpha_=_0.001"),
    // new ExternalAlgorithmPcalgPc("CPC_pcalg_defaults_alpha_=_0.001"),
    // new ExternalAlgorithmPcalgPc("CPC_majority_pcalg_defaults_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 ElapsedTime());
    // 
    comparison.generateReportFromExternalAlgorithms("/Users/user/comparison-data/condition_2", "/Users/user/causal-comparisons/condition_2", "Counts.txt", algorithms, statistics2, parameters);
}

Example 39 with Parameters

use of edu.cmu.tetrad.util.Parameters in project tetrad by cmu-phil.

the class ExampleSave method main.

public static void main(String... args) {
    Parameters parameters = new Parameters();
    parameters.set("numRuns", 10);
    parameters.set("numMeasures", 50, 100, 500);
    parameters.set("avgDegree", 2, 4, 6);
    parameters.set("sampleSize", 100, 500, 1000);
    parameters.set("differentGraphs", true);
    parameters.set("maxDegree", 100);
    parameters.set("maxIndegree", 100);
    parameters.set("maxOutdegree", 100);
    parameters.set("connected", false);
    parameters.set("coefLow", 0.2);
    parameters.set("coefHigh", 0.9);
    parameters.set("coefSymmetric", true);
    parameters.set("varLow", 1);
    parameters.set("varHigh", 3);
    parameters.set("randomizeColumns", true);
    NumberFormatUtil.getInstance().setNumberFormat(new DecimalFormat("0.000000"));
    Simulation simulation = new SemSimulation(new RandomForward());
    Comparison comparison = new Comparison();
    comparison.saveToFiles("/Users/user/comparison-data/condition_2", simulation, parameters);
}

Example 40 with Parameters

use of edu.cmu.tetrad.util.Parameters in project tetrad by cmu-phil.

the class ExampleFirstInflection method main.

public static void main(String... args) {
    Parameters parameters = new Parameters();
    parameters.set("numMeasures", 40, 100);
    parameters.set("avgDegree", 2);
    parameters.set("sampleSize", 400, 800);
    parameters.set("numRuns", 10);
    parameters.set("differentGraphs", true);
    parameters.set("numLatents", 0);
    parameters.set("maxDegree", 100);
    parameters.set("maxIndegree", 100);
    parameters.set("maxOutdegree", 100);
    parameters.set("connected", false);
    parameters.set("coefLow", 0.2);
    parameters.set("coefHigh", 0.9);
    parameters.set("varLow", 1);
    parameters.set("varHigh", 3);
    parameters.set("verbose", false);
    parameters.set("coefSymmetric", true);
    parameters.set("percentDiscrete", 0);
    parameters.set("numCategories", 3);
    parameters.set("differentGraphs", true);
    parameters.set("intervalBetweenShocks", 10);
    parameters.set("intervalBetweenRecordings", 10);
    parameters.set("fisherEpsilon", 0.001);
    parameters.set("randomizeColumns", true);
    parameters.set("alpha", 1e-8);
    parameters.set("depth", -1);
    parameters.set("penaltyDiscount", 4);
    parameters.set("useMaxPOrientationHeuristic", false);
    parameters.set("maxPOrientationMaxPathLength", 3);
    parameters.set("verbose", false);
    parameters.set("scaleFreeAlpha", 0.00001);
    parameters.set("scaleFreeBeta", 0.4);
    parameters.set("scaleFreeDeltaIn", .1);
    parameters.set("scaleFreeDeltaOut", 3);
    parameters.set("symmetricFirstStep", false);
    parameters.set("faithfulnessAssumed", true);
    parameters.set("maxDegree", 100);
    // parameters.set("logScale", true);
    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 ElapsedTime());
    statistics.setWeight("AP", 0.25);
    statistics.setWeight("AR", 0.25);
    statistics.setWeight("AHP", 0.25);
    statistics.setWeight("AHR", 0.25);
    Algorithms algorithms = new Algorithms();
    Algorithm fges = new Fges(new SemBicScore());
    // algorithms.add(new FirstInflection(fges, "alpha", -7, -2, -.5));
    algorithms.add(new FirstInflection(fges, "penaltyDiscount", 0.7, 5, 1));
    Simulations simulations = new Simulations();
    simulations.add(new LinearFisherModel(new RandomForward()));
    Comparison comparison = new Comparison();
    comparison.setShowAlgorithmIndices(true);
    comparison.setShowSimulationIndices(true);
    comparison.setSortByUtility(false);
    comparison.setShowUtilities(false);
    comparison.setParallelized(true);
    comparison.setComparisonGraph(Comparison.ComparisonGraph.Pattern_of_the_true_DAG);
    comparison.compareFromSimulations("first.inflection", simulations, algorithms, statistics, parameters);
}