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

Example 21 with Parameters

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

the class SemEstimatorWrapper method serializableInstance.

// public SemEstimatorWrapper(DataWrapper dataWrapper,
// SemPmWrapper semPmWrapper,
// SemImWrapper semImWrapper,
// Parameters params) {
// if (dataWrapper == null) {
// throw new NullPointerException();
// }
// 
// if (semPmWrapper == null) {
// throw new NullPointerException();
// }
// 
// if (semImWrapper == null) {
// throw new NullPointerException();
// }
// 
// DataSet dataSet =
// (DataSet) dataWrapper.getSelectedDataModel();
// SemPm semPm = semPmWrapper.getSemPm();
// SemIm semIm = semImWrapper.getSemIm();
// 
// this.semEstimator = new SemEstimator(dataSet, semPm, getOptimizer());
// if (!degreesOfFreedomCheck(semPm)) return;
// this.semEstimator.setTrueSemIm(semIm);
// this.semEstimator.setNumRestarts(getParams().getInt("numRestarts", 1));
// this.semEstimator.estimate();
// 
// this.params = params;
// 
// log();
// }
/**
 * Generates a simple exemplar of this class to test serialization.
 *
 * @see TetradSerializableUtils
 */
public static SemEstimatorWrapper serializableInstance() {
    List<Node> variables = new LinkedList<>();
    ContinuousVariable x = new ContinuousVariable("X");
    variables.add(x);
    DataSet dataSet = new ColtDataSet(10, variables);
    for (int i = 0; i < dataSet.getNumRows(); i++) {
        for (int j = 0; j < dataSet.getNumColumns(); j++) {
            dataSet.setDouble(i, j, RandomUtil.getInstance().nextDouble());
        }
    }
    Dag dag = new Dag();
    dag.addNode(x);
    SemPm pm = new SemPm(dag);
    Parameters params1 = new Parameters();
    return new SemEstimatorWrapper(dataSet, pm, params1);
}

Example 22 with Parameters

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

the class MbFanSearchRunner method getIndependenceTest.

public IndependenceTest getIndependenceTest() {
    Object dataModel = getDataModel();
    if (dataModel == null) {
        dataModel = getSourceGraph();
    }
    Parameters params = getParams();
    IndTestType testType = (IndTestType) params.get("indTestType", IndTestType.FISHER_Z);
    return new IndTestChooser().getTest(dataModel, params, testType);
}

Example 23 with Parameters

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

the class LingamStructureRunner method execute.

// ============================PUBLIC METHODS==========================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    DataModel source = getDataModel();
    if (!(source instanceof DataSet)) {
        throw new IllegalArgumentException("Expecting a rectangular data set.");
    }
    DataSet data = (DataSet) source;
    if (!data.isContinuous()) {
        throw new IllegalArgumentException("Expecting a continuous data set.");
    }
    // Lingam_old lingam = new Lingam_old();
    // lingam.setAlternativePenalty(getParameters().getAlternativePenalty());
    // lingam.setPruningDone(true);
    // lingam.setAlternativePenalty(getParameters().getAlternativePenalty());
    // GraphWithParameters result = lingam.lingam(data);
    // Graph graph = result.getGraph();
    Lingam lingam = new Lingam();
    Parameters params = getParams();
    Graph graph = lingam.search(data);
    setResultGraph(graph);
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
}

Example 24 with Parameters

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

the class PcStableMaxLocalRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
public void execute() {
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    IndependenceTest independenceTest = getIndependenceTest();
    Parameters testParams = getParams();
    PcStableMaxLocal search = new PcStableMaxLocal(independenceTest);
    search.setAggressivelyPreventCycles(isAggressivelyPreventCycles());
    search.setKnowledge(knowledge);
    Graph graph = search.search();
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else if (knowledge.isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    setResultGraph(graph);
}

Example 25 with Parameters

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

the class CeFanSearchRunner method getIndependenceTest.

public IndependenceTest getIndependenceTest() {
    Object dataModel = getDataModel();
    if (dataModel == null) {
        dataModel = getSourceGraph();
    }
    Parameters params = getParams();
    IndTestType testType = (IndTestType) params.get("indTestType", IndTestType.FISHER_Z);
    return new IndTestChooser().getTest(dataModel, params, testType);
}