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

Example 56 with SemIm

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

the class TestDeltaTetradTest method test4aIteratedPositives.

@Test
public void test4aIteratedPositives() {
    RandomUtil.getInstance().setSeed(482834823L);
    int numTrials = 10;
    double alpha = 0.2;
    SemIm sem = getFigure4aSem();
    int[] sampleSizes = new int[] { 100, 500, 1000, 5000 };
    double[][] answers = { { .1, .5, .2, .1, .1, .1 }, { 0.1, 0.6, 0.0, 0.0, 0.0, 0.0 }, { 0.1, 0.7, 0.2, 0.2, 0.2, 0.2 }, { 0.3, 0.7, 0.2, 0.1, 0.1, 0.1 } };
    for (int i = 0; i < 4; i++) {
        System.out.println("i = " + i);
        int sampleSize = sampleSizes[i];
        int[] count = new int[6];
        for (int k = 0; k < numTrials; k++) {
            DataSet data = sem.simulateData(sampleSize, false);
            Node x1 = data.getVariable("x1");
            Node x2 = data.getVariable("x2");
            Node x3 = data.getVariable("x3");
            Node x4 = data.getVariable("x4");
            Tetrad t1234 = new Tetrad(x1, x2, x3, x4);
            Tetrad t1342 = new Tetrad(x1, x3, x4, x2);
            Tetrad t1423 = new Tetrad(x1, x4, x2, x3);
            DeltaTetradTest test = new DeltaTetradTest(new CorrelationMatrix(data));
            double p1 = test.getPValue(t1234);
            double p2 = test.getPValue(t1342);
            double p3 = test.getPValue(t1423);
            double p4 = test.getPValue(t1234, t1342);
            double p5 = test.getPValue(t1234, t1423);
            double p6 = test.getPValue(t1342, t1423);
            if (p1 < alpha)
                count[0]++;
            if (p2 < alpha)
                count[1]++;
            if (p3 < alpha)
                count[2]++;
            if (p4 < alpha)
                count[3]++;
            if (p5 < alpha)
                count[4]++;
            if (p6 < alpha)
                count[5]++;
        }
        double[] _answer = new double[6];
        for (int j = 0; j < 6; j++) {
            double v = count[j] / (double) numTrials;
            _answer[j] = v;
        }
    // System.out.println(MatrixUtils.toString(_answer));
    // System.out.println(MatrixUtils.toString(answers[i]));
    // assertTrue(Arrays.equals(_answer, answers[i]));
    }
}

Example 57 with SemIm

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

the class TestDeltaTetradTest method getFigure4bSem.

private SemIm getFigure4bSem() {
    Graph graph = new EdgeListGraph();
    Node xi1 = new GraphNode("xi1");
    Node xi2 = new GraphNode("xi2");
    Node x1 = new GraphNode("x1");
    Node x2 = new GraphNode("x2");
    Node x3 = new GraphNode("x3");
    Node x4 = new GraphNode("x4");
    graph.addNode(xi1);
    graph.addNode(xi2);
    graph.addNode(x1);
    graph.addNode(x2);
    graph.addNode(x3);
    graph.addNode(x4);
    graph.addDirectedEdge(xi1, x1);
    graph.addDirectedEdge(xi1, x2);
    graph.addDirectedEdge(xi2, x3);
    graph.addDirectedEdge(xi2, x4);
    graph.addDirectedEdge(xi1, xi2);
    SemPm pm = new SemPm(graph);
    return new SemIm(pm);
}

Example 58 with SemIm

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

the class TestStandardizedSem method test1.

// Test the code that standardizes a data set.
@Test
public void test1() {
    List<Node> nodes = new ArrayList<>();
    for (int i = 0; i < 5; i++) {
        nodes.add(new ContinuousVariable("X" + (i + 1)));
    }
    SemGraph graph = new SemGraph(new Dag(GraphUtils.randomGraph(nodes, 0, 5, 30, 15, 15, false)));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet dataSet = im.simulateData(1000, false);
    TetradMatrix _dataSet = dataSet.getDoubleData();
    _dataSet = DataUtils.standardizeData(_dataSet);
    DataSet dataSetStandardized = ColtDataSet.makeData(dataSet.getVariables(), _dataSet);
    DataUtils.cov(_dataSet);
    DataUtils.mean(_dataSet);
    SemEstimator estimator = new SemEstimator(dataSetStandardized, pm);
    SemIm imStandardized = estimator.estimate();
    imStandardized.getEdgeCoef();
    imStandardized.getErrCovar();
    new TetradVector(imStandardized.getMeans());
    imStandardized.getEdgeCoef();
    imStandardized.getErrCovar();
    StandardizedSemIm sem = new StandardizedSemIm(im);
    imStandardized.getEdgeCoef();
    imStandardized.getErrCovar();
    assertTrue(isStandardized(sem));
}

Example 59 with SemIm

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

the class TestStandardizedSem method test4.

// This tests what the user is going to try to do in the GUI.
@Test
public void test4() {
    List<Node> nodes = new ArrayList<>();
    for (int i1 = 0; i1 < 10; i1++) {
        nodes.add(new ContinuousVariable("X" + (i1 + 1)));
    }
    SemGraph graph = new SemGraph(new Dag(GraphUtils.randomGraph(nodes, 0, 10, 30, 15, 15, false)));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    StandardizedSemIm sem = new StandardizedSemIm(im);
    for (int i = 0; i < 20; i++) {
        List<Edge> edges = new ArrayList<>(graph.getEdges());
        RandomUtil random = RandomUtil.getInstance();
        int index = random.nextInt(edges.size());
        Edge edge = edges.get(index);
        Node a = edge.getNode1();
        Node b = edge.getNode2();
        StandardizedSemIm.ParameterRange range = sem.getCoefficientRange(a, b);
        double high = range.getHigh();
        double low = range.getLow();
        double coef = low + random.nextDouble() * (high - low);
        assertTrue(sem.setEdgeCoefficient(a, b, coef));
        coef = high + random.nextDouble() * (high - low);
        assertFalse(sem.setEdgeCoefficient(a, b, coef));
        coef = low - random.nextDouble() * (high - low);
        assertFalse(sem.setEdgeCoefficient(a, b, coef));
    }
}

Example 60 with SemIm

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

the class TestStandardizedSem method test3.

@Test
public void test3() {
    RandomUtil.getInstance().setSeed(582374923L);
    SemGraph graph = new SemGraph();
    Node x1 = new ContinuousVariable("X1");
    Node x2 = new ContinuousVariable("X2");
    Node x3 = new ContinuousVariable("X3");
    graph.addNode(x1);
    graph.addNode(x2);
    graph.addNode(x3);
    graph.setShowErrorTerms(true);
    graph.addDirectedEdge(x1, x3);
    graph.addDirectedEdge(x2, x3);
    graph.addDirectedEdge(x1, x2);
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    StandardizedSemIm sem = new StandardizedSemIm(im);
    DataSet data = sem.simulateData(5000, false);
    assertFalse(sem.setEdgeCoefficient(x1, x2, 1.2));
    assertFalse(sem.setEdgeCoefficient(x1, x2, 1.5));
    assertTrue(sem.setEdgeCoefficient(x1, x2, .5));
    assertTrue(sem.setEdgeCoefficient(x1, x3, -.1));
    assertTrue(isStandardized(sem));
}