Examples with SemBicScoreDeterministic edu.cmu.tetrad.search.SemBicScoreDeterministic used on opensource projects

Example 1 with SemBicScoreDeterministic

use of edu.cmu.tetrad.search.SemBicScoreDeterministic in project tetrad by cmu-phil.

the class Pcd method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        IndTestScore test;
        if (dataSet instanceof ICovarianceMatrix) {
            SemBicScoreDeterministic score = new SemBicScoreDeterministic((ICovarianceMatrix) dataSet);
            score.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
            score.setDeterminismThreshold(parameters.getDouble("determinismThreshold"));
            test = new IndTestScore(score);
        } else if (dataSet instanceof DataSet) {
            SemBicScoreDeterministic score = new SemBicScoreDeterministic(new CovarianceMatrix((DataSet) dataSet));
            score.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
            score.setDeterminismThreshold(parameters.getDouble("determinismThreshold"));
            test = new IndTestScore(score);
        } else {
            throw new IllegalArgumentException("Expecting a dataset or a covariance matrix.");
        }
        edu.cmu.tetrad.search.Pcd search = new edu.cmu.tetrad.search.Pcd(test);
        search.setDepth(parameters.getInt("depth"));
        search.setKnowledge(knowledge);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    } else {
        Pcd algorithm = new Pcd();
        // algorithm.setKnowledge(knowledge);
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, algorithm, parameters.getInt("bootstrapSampleSize"));
        search.setKnowledge(knowledge);
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}

Example 2 with SemBicScoreDeterministic

use of edu.cmu.tetrad.search.SemBicScoreDeterministic in project tetrad by cmu-phil.

the class SemBicDTest method getTest.

@Override
public IndependenceTest getTest(DataModel dataSet, Parameters parameters) {
    SemBicScoreDeterministic score = new SemBicScoreDeterministic(new CovarianceMatrix((ICovarianceMatrix) dataSet));
    score.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
    return new IndTestScore(score, dataSet);
}

Example 3 with SemBicScoreDeterministic

use of edu.cmu.tetrad.search.SemBicScoreDeterministic in project tetrad by cmu-phil.

the class FgesD method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        if (algorithm != null) {
        // initialGraph = algorithm.search(dataSet, parameters);
        }
        edu.cmu.tetrad.search.FgesD search;
        if (dataSet instanceof ICovarianceMatrix) {
            SemBicScoreDeterministic score = new SemBicScoreDeterministic((ICovarianceMatrix) dataSet);
            score.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
            score.setDeterminismThreshold(parameters.getDouble("determinismThreshold"));
            search = new edu.cmu.tetrad.search.FgesD(score);
        } else if (dataSet instanceof DataSet) {
            SemBicScoreDeterministic score = new SemBicScoreDeterministic(new CovarianceMatrix((DataSet) dataSet));
            score.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
            score.setDeterminismThreshold(parameters.getDouble("determinismThreshold"));
            search = new edu.cmu.tetrad.search.FgesD(score);
        } else {
            throw new IllegalArgumentException("Expecting a dataset or a covariance matrix.");
        }
        search.setFaithfulnessAssumed(parameters.getBoolean("faithfulnessAssumed"));
        search.setKnowledge(knowledge);
        search.setVerbose(parameters.getBoolean("verbose"));
        search.setMaxDegree(parameters.getInt("maxDegree"));
        // search.setSymmetricFirstStep(parameters.getBoolean("symmetricFirstStep"));
        Object obj = parameters.get("printStedu.cmream");
        if (obj instanceof PrintStream) {
            search.setOut((PrintStream) obj);
        }
        if (initialGraph != null) {
            search.setInitialGraph(initialGraph);
        }
        return search.search();
    } else {
        FgesD algorithm = new FgesD();
        // algorithm.setKnowledge(knowledge);
        if (initialGraph != null) {
            algorithm.setInitialGraph(initialGraph);
        }
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, algorithm, parameters.getInt("bootstrapSampleSize"));
        search.setKnowledge(knowledge);
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}