Examples with ColtDataSet edu.cmu.tetrad.data.ColtDataSet used on opensource projects

Example 16 with ColtDataSet

use of edu.cmu.tetrad.data.ColtDataSet in project tetrad by cmu-phil.

the class DirichletBayesIm method simulateDataHelper.

/**
 * Simulates a sample with the given sample size.
 *
 * @param sampleSize      the sample size.
 * @param randomUtil      optional random number generator to use when
 *                        creating the data
 * @param latentDataSaved true iff data for latent variables should be
 *                        saved.
 * @return the simulated sample as a DataSet.
 */
private DataSet simulateDataHelper(int sampleSize, RandomUtil randomUtil, boolean latentDataSaved) {
    int numMeasured = 0;
    int[] map = new int[nodes.length];
    List<Node> variables = new LinkedList<>();
    for (int j = 0; j < nodes.length; j++) {
        if (!latentDataSaved && nodes[j].getNodeType() != NodeType.MEASURED) {
            continue;
        }
        int numCategories = bayesPm.getNumCategories(nodes[j]);
        List<String> categories = new LinkedList<>();
        for (int k = 0; k < numCategories; k++) {
            categories.add(bayesPm.getCategory(nodes[j], k));
        }
        DiscreteVariable var = new DiscreteVariable(nodes[j].getName(), categories);
        variables.add(var);
        int index = ++numMeasured - 1;
        map[index] = j;
    }
    DataSet dataSet = new ColtDataSet(sampleSize, variables);
    constructSample(sampleSize, randomUtil, numMeasured, dataSet, map);
    return dataSet;
}

Example 17 with ColtDataSet

use of edu.cmu.tetrad.data.ColtDataSet in project tetrad by cmu-phil.

the class GraphComparisonParams method newExecution.

// ==========================PUBLIC METHODS===========================//
public final void newExecution() {
    ContinuousVariable adjCorrect = new ContinuousVariable("ADJ_COR");
    ContinuousVariable adjFn = new ContinuousVariable("ADJ_FN");
    ContinuousVariable adjFp = new ContinuousVariable("ADJ_FP");
    ContinuousVariable arrowptCorrect = new ContinuousVariable("AHD_COR");
    ContinuousVariable arrowptFn = new ContinuousVariable("AHD_FN");
    ContinuousVariable arrowptFp = new ContinuousVariable("AHD_FP");
    ContinuousVariable adjPrec = new ContinuousVariable("ADJ_PREC");
    ContinuousVariable adjRec = new ContinuousVariable("ADJ_REC");
    ContinuousVariable arrowptPrec = new ContinuousVariable("ARROWPT_PREC");
    ContinuousVariable arrowptRec = new ContinuousVariable("ARROWPT_REC");
    ContinuousVariable shd = new ContinuousVariable("SHD");
    // ContinuousVariable twoCycleCorrect = new ContinuousVariable("TC_COR");
    // ContinuousVariable twoCycleFn = new ContinuousVariable("TC_FN");
    // ContinuousVariable twoCycleFp = new ContinuousVariable("TC_FP");
    List<Node> variables = new LinkedList<>();
    variables.add(adjCorrect);
    variables.add(adjFn);
    variables.add(adjFp);
    variables.add(arrowptCorrect);
    variables.add(arrowptFn);
    variables.add(arrowptFp);
    variables.add(adjPrec);
    variables.add(adjRec);
    variables.add(arrowptPrec);
    variables.add(arrowptRec);
    variables.add(shd);
    // variables.add(twoCycleCorrect);
    // variables.add(twoCycleFn);
    // variables.add(twoCycleFp);
    dataSet = new ColtDataSet(0, variables);
    dataSet.setNumberFormat(new DecimalFormat("0"));
}

Example 18 with ColtDataSet

use of edu.cmu.tetrad.data.ColtDataSet in project tetrad by cmu-phil.

the class TestDataWrapper method testDataModelList.

@Test
public void testDataModelList() {
    DataModelList modelList = new DataModelList();
    List<Node> variables1 = new ArrayList<>();
    for (int i = 0; i < 10; i++) {
        variables1.add(new ContinuousVariable("X" + i));
    }
    List<Node> variables2 = new ArrayList<>();
    for (int i = 0; i < 10; i++) {
        variables2.add(new ContinuousVariable("X" + i));
    }
    DataSet first = new ColtDataSet(10, variables1);
    first.setName("first");
    DataSet second = new ColtDataSet(10, variables2);
    second.setName("second");
    modelList.add(first);
    modelList.add(second);
    assertTrue(modelList.contains(first));
    assertTrue(modelList.contains(second));
    modelList.setSelectedModel(second);
    try {
        DataModelList modelList2 = new MarshalledObject<>(modelList).get();
        assertEquals("second", modelList2.getSelectedModel().getName());
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 19 with ColtDataSet

use of edu.cmu.tetrad.data.ColtDataSet in project tetrad by cmu-phil.

the class LogisticRegressionRunner method serializableInstance.

/**
 * Generates a simple exemplar of this class to test serialization.
 *
 * @see TetradSerializableUtils
 */
public static LogisticRegressionRunner serializableInstance() {
    List<Node> variables = new LinkedList<>();
    ContinuousVariable var1 = new ContinuousVariable("X");
    ContinuousVariable var2 = new ContinuousVariable("Y");
    variables.add(var1);
    variables.add(var2);
    DataSet dataSet = new ColtDataSet(3, variables);
    double[] col1data = new double[] { 0.0, 1.0, 2.0 };
    double[] col2data = new double[] { 2.3, 4.3, 2.5 };
    for (int i = 0; i < 3; i++) {
        dataSet.setDouble(i, 0, col1data[i]);
        dataSet.setDouble(i, 1, col2data[i]);
    }
    DataWrapper dataWrapper = new DataWrapper(dataSet);
    return new LogisticRegressionRunner(dataWrapper, new Parameters());
}

Example 20 with ColtDataSet

use of edu.cmu.tetrad.data.ColtDataSet in project tetrad by cmu-phil.

the class TestTransform method testTransformWithNewColumnVariable.

@Test
public void testTransformWithNewColumnVariable() {
    List<Node> list = Arrays.asList((Node) new ContinuousVariable("x"), new ContinuousVariable("y"));
    DataSet data = new ColtDataSet(1, list);
    data.setDouble(0, 0, 1);
    data.setDouble(1, 0, 1);
    data.setDouble(0, 1, 1);
    data.setDouble(1, 1, 1);
    try {
        String eq = "w = (x + y) * x";
        Transformation.transform(data, eq);
        assertTrue(data.getDouble(0, 2) == 2.0);
        assertTrue(data.getDouble(0, 2) == 2.0);
    } catch (Exception ex) {
        ex.printStackTrace();
        fail(ex.getMessage());
    }
}