Examples with SemPm edu.cmu.tetrad.sem.SemPm used on opensource projects

Example 6 with SemPm

use of edu.cmu.tetrad.sem.SemPm in project tetrad by cmu-phil.

the class TestDM method test10.

// 
@Test
public void test10() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(5);
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X2"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X4"));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(100000, false);
    DMSearch search = new DMSearch();
    search.setUseFges(false);
    search.setInputs(new int[] { 0, 1 });
    search.setOutputs(new int[] { 2, 3, 4 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    search.search();
    print("Test Case 10");
    // Trying to quiet the output for unit tests.
    if (false) {
        System.out.println(search.getDmStructure());
    }
    assertTrue(true);
}

Example 7 with SemPm

use of edu.cmu.tetrad.sem.SemPm in project tetrad by cmu-phil.

the class TestCpc method test7.

@Test
public void test7() {
    int numVars = 6;
    int numEdges = 6;
    List<Node> nodes = new ArrayList<>();
    for (int i = 0; i < numVars; i++) {
        nodes.add(new ContinuousVariable("X" + (i + 1)));
    }
    Dag trueGraph = new Dag(GraphUtils.randomGraph(nodes, 0, numEdges, 7, 5, 5, false));
    SemPm semPm = new SemPm(trueGraph);
    SemIm semIm = new SemIm(semPm);
    DataSet _dataSet = semIm.simulateData(1000, false);
    IndependenceTest test = new IndTestFisherZ(_dataSet, 0.05);
    Cpc search = new Cpc(test);
    Graph resultGraph = search.search();
}

Example 8 with SemPm

use of edu.cmu.tetrad.sem.SemPm in project tetrad by cmu-phil.

the class TestIndTestFisherZ method test2.

@Test
public void test2() {
    for (int p = 0; p < 50; p++) {
        Graph graph = new EdgeListGraph();
        Node x = new ContinuousVariable("X");
        Node y = new ContinuousVariable("Y");
        Node w1 = new ContinuousVariable("W1");
        Node w2 = new ContinuousVariable("W2");
        Node w3 = new ContinuousVariable("W3");
        Node r = new ContinuousVariable("R");
        graph.addNode(x);
        graph.addNode(y);
        graph.addNode(w1);
        graph.addNode(w2);
        graph.addNode(w3);
        graph.addNode(r);
        graph.addDirectedEdge(x, w1);
        graph.addDirectedEdge(w1, w2);
        graph.addDirectedEdge(w2, y);
        graph.addDirectedEdge(w3, y);
        // graph.addDirectedEdge(x, r);
        // graph.addDirectedEdge(r, y);
        graph.addDirectedEdge(y, r);
        // 
        SemPm pm = new SemPm(graph);
        Parameters parameters = new Parameters();
        parameters.set("coefLow", .3);
        parameters.set("coefHigh", .8);
        parameters.set("coefSymmetric", false);
        SemIm im = new SemIm(pm, parameters);
        final int N = 1000;
        DataSet data = im.simulateData(N, false);
        ICovarianceMatrix _cov = new CovarianceMatrix(data);
        TetradMatrix cov = _cov.getMatrix();
        List<Node> nodes = _cov.getVariables();
        final int xi = nodes.indexOf(x);
        final int yi = nodes.indexOf(y);
        final int ri = nodes.indexOf(r);
        double xy = StatUtils.partialCorrelation(cov, xi, yi);
        double xyr = StatUtils.partialCorrelation(cov, xi, yi, ri);
        double f1 = 0.5 * sqrt(N - 3) * log(1. + xy) - log(1. - xy);
        double f2 = 0.5 * sqrt(N - 3 - 1) * log(1. + xyr) - log(1. - xyr);
        System.out.println(abs(f1) > abs(f2));
    }
}

Example 9 with SemPm

use of edu.cmu.tetrad.sem.SemPm in project tetrad by cmu-phil.

the class TestDataLoadersRoundtrip method testContinuousRoundtrip.

@Test
public void testContinuousRoundtrip() {
    setUp();
    try {
        List<Node> nodes = new ArrayList<>();
        for (int i = 0; i < 5; i++) {
            nodes.add(new ContinuousVariable("X" + (i + 1)));
        }
        Graph randomGraph = new Dag(GraphUtils.randomGraph(nodes, 0, 5, 30, 15, 15, false));
        SemPm semPm1 = new SemPm(randomGraph);
        SemIm semIm1 = new SemIm(semPm1);
        DataSet dataSet = semIm1.simulateData(10, false);
        FileWriter fileWriter = new FileWriter("target/test_data/roundtrip.dat");
        Writer writer = new PrintWriter(fileWriter);
        DataWriter.writeRectangularData(dataSet, writer, ',');
        writer.close();
        // 
        new File("test_data").mkdir();
        File file = new File("target/test_data/roundtrip.dat");
        DataReader reader = new DataReader();
        reader.setDelimiter(DelimiterType.COMMA);
        DataSet _dataSet = reader.parseTabular(file);
        assertTrue(dataSet.equals(_dataSet));
    } catch (IOException e) {
        e.printStackTrace();
        fail();
    }
}

Example 10 with SemPm

use of edu.cmu.tetrad.sem.SemPm 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);
}