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

Example 61 with SemIm

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

the class TestStandardizedSem method test7.

// This tests what the user is going to try to do in the GUI.
@Test
public void test7() {
    RandomUtil random = RandomUtil.getInstance();
    random.setSeed(9394929393L);
    List<Node> nodes1 = new ArrayList<>();
    for (int i1 = 0; i1 < 5; i1++) {
        nodes1.add(new ContinuousVariable("X" + (i1 + 1)));
    }
    SemGraph graph = new SemGraph(new Dag(GraphUtils.randomGraph(nodes1, 0, 5, 30, 15, 15, false)));
    List<Node> nodes = graph.getNodes();
    int n1 = RandomUtil.getInstance().nextInt(nodes.size());
    int n2 = RandomUtil.getInstance().nextInt(nodes.size());
    while (n1 == n2) {
        n2 = RandomUtil.getInstance().nextInt(nodes.size());
    }
    Node node1 = nodes.get(n1);
    Node node2 = nodes.get(n2);
    Edge _edge = Edges.bidirectedEdge(node1, node2);
    graph.addEdge(_edge);
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    StandardizedSemIm sem = new StandardizedSemIm(im);
    DataSet data3 = sem.simulateDataReducedForm(1000, false);
    graph.setShowErrorTerms(false);
    for (int i = 0; i < 1; i++) {
        for (Edge edge : graph.getEdges()) {
            Node a = edge.getNode1();
            Node b = edge.getNode2();
            if (Edges.isDirectedEdge(edge)) {
                double initial = sem.getEdgeCoef(a, b);
                StandardizedSemIm.ParameterRange range = sem.getCoefficientRange(a, b);
                assertEquals(initial, sem.getEdgeCoef(a, b), 0.1);
                double low = range.getLow();
                double high = range.getHigh();
                double _coef = sem.getEdgeCoef(a, b);
                double coef = low + random.nextDouble() * (high - low);
                assertTrue(sem.setEdgeCoefficient(a, b, coef));
                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));
            } else if (Edges.isBidirectedEdge(edge)) {
                sem.setErrorCovariance(node1, node2, .15);
                assertTrue(isStandardized(sem));
                StandardizedSemIm.ParameterRange range2 = sem.getCovarianceRange(a, b);
                double low = range2.getLow();
                double high = range2.getHigh();
                if (low == Double.NEGATIVE_INFINITY)
                    low = -10000;
                if (high == Double.POSITIVE_INFINITY)
                    high = 10000;
                double _coef = sem.getErrorCovariance(a, b);
                double coef = low + random.nextDouble() * (high - low);
                assertTrue(sem.setErrorCovariance(a, b, coef));
                sem.setErrorCovariance(a, b, _coef);
                if (high != 10000) {
                    coef = high + random.nextDouble() * (high - low);
                    assertFalse(sem.setErrorCovariance(a, b, coef));
                }
                if (low != -10000) {
                    coef = low - random.nextDouble() * (high - low);
                    assertFalse(sem.setErrorCovariance(a, b, coef));
                }
            }
        }
    }
}

Example 62 with SemIm

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

the class TestSemEvidence method testSemEvidence.

@Test
public void testSemEvidence() {
    Graph graph = constructGraph1();
    SemPm semPm = new SemPm(graph);
    SemIm semIm = new SemIm(semPm);
    SemEvidence evidence = new SemEvidence(semIm);
    evidence.setManipulated(1, true);
    assertTrue(evidence.isManipulated(1));
}

Example 63 with SemIm

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

the class TestSemUpdater method testUpdate.

@Test
public void testUpdate() {
    Graph graph = constructGraph1();
    SemPm semPm = new SemPm(graph);
    SemIm semIm = new SemIm(semPm);
    List<Node> nodes = semIm.getVariableNodes();
    SemUpdater semUpdater = new SemUpdater(semIm);
    SemEvidence evidence = new SemEvidence(semIm);
    evidence.getProposition().setValue(nodes.get(4), 10.0);
    evidence.getProposition().setValue(nodes.get(2), 1.5);
    semUpdater.setEvidence(evidence);
    evidence.setManipulated(1, true);
    semUpdater.getManipulatedSemIm();
    semUpdater.getUpdatedSemIm();
}

Example 64 with SemIm

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

the class TestSemXml method sampleSemIm1.

private static SemIm sampleSemIm1() {
    List<Node> nodes = new ArrayList<>();
    for (int i = 0; i < 5; i++) {
        nodes.add(new ContinuousVariable("X" + (i + 1)));
    }
    Graph graph = new Dag(GraphUtils.randomGraph(nodes, 0, 5, 30, 15, 15, true));
    SemPm pm = new SemPm(graph);
    return new SemIm(pm);
}

Example 65 with SemIm

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

the class TestStatUtils method testConditionalCorrelation.

/**
 * Tests that the unconditional correlations and covariances are correct,
 * at least for the unconditional tests.
 */
@Test
public void testConditionalCorrelation() {
    RandomUtil.getInstance().setSeed(30299533L);
    // Make sure the unconditional correlations and covariances are OK.
    List<Node> nodes1 = new ArrayList<>();
    for (int i = 0; i < 5; i++) {
        nodes1.add(new ContinuousVariable("X" + (i + 1)));
    }
    Graph graph = new Dag(GraphUtils.randomGraph(nodes1, 0, 5, 3, 3, 3, false));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet dataSet = im.simulateData(1000, false);
    double[] x = dataSet.getDoubleData().getColumn(0).toArray();
    double[] y = dataSet.getDoubleData().getColumn(1).toArray();
    double r1 = StatUtils.correlation(x, y);
    double s1 = StatUtils.covariance(x, y);
    double v1 = StatUtils.variance(x);
    double sd1 = StatUtils.sd(x);
    ICovarianceMatrix cov = new CovarianceMatrix(dataSet);
    TetradMatrix _cov = cov.getMatrix();
    double r2 = StatUtils.partialCorrelation(_cov, 0, 1);
    double s2 = StatUtils.partialCovariance(_cov, 0, 1);
    double v2 = StatUtils.partialVariance(_cov, 0);
    double sd2 = StatUtils.partialStandardDeviation(_cov, 0);
    assertEquals(r1, r2, .1);
    assertEquals(s1, s2, .1);
    assertEquals(v1, v2, .1);
    assertEquals(sd1, sd2, 0.1);
}