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

Example 51 with SemPm

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

the class TestDiscretizer method testManualDiscretize3.

@Test
public void testManualDiscretize3() {
    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 data = im.simulateData(100, false);
    List<Node> nodes = data.getVariables();
    Discretizer discretizer = new Discretizer(data);
    discretizer.setVariablesCopied(true);
    discretizer.setVariablesCopied(true);
    discretizer.equalCounts(nodes.get(0), 3);
    DataSet discretized = discretizer.discretize();
    assertTrue(discretized.getVariable(0) instanceof DiscreteVariable);
    assertTrue(discretized.getVariable(1) instanceof ContinuousVariable);
    assertTrue(discretized.getVariable(2) instanceof ContinuousVariable);
    assertTrue(discretized.getVariable(3) instanceof ContinuousVariable);
    assertTrue(discretized.getVariable(4) instanceof ContinuousVariable);
}

Example 52 with SemPm

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

the class TestIndTestFisherZ method testDirections.

@Test
public void testDirections() {
    RandomUtil.getInstance().setSeed(48285934L);
    Graph graph1 = new EdgeListGraph();
    Graph graph2 = new EdgeListGraph();
    Node x = new GraphNode("X");
    Node y = new GraphNode("Y");
    Node z = new GraphNode("Z");
    graph1.addNode(x);
    graph1.addNode(y);
    graph1.addNode(z);
    graph2.addNode(x);
    graph2.addNode(y);
    graph2.addNode(z);
    graph1.addEdge(Edges.directedEdge(x, y));
    graph1.addEdge(Edges.directedEdge(y, z));
    graph2.addEdge(Edges.directedEdge(x, y));
    graph2.addEdge(Edges.directedEdge(z, y));
    SemPm pm1 = new SemPm(graph1);
    SemPm pm2 = new SemPm(graph2);
    SemIm im1 = new SemIm(pm1);
    SemIm im2 = new SemIm(pm2);
    im2.setEdgeCoef(x, y, im1.getEdgeCoef(x, y));
    im2.setEdgeCoef(z, y, im1.getEdgeCoef(y, z));
    DataSet data1 = im1.simulateData(500, false);
    DataSet data2 = im2.simulateData(500, false);
    IndependenceTest test1 = new IndTestFisherZ(data1, 0.05);
    IndependenceTest test2 = new IndTestFisherZ(data2, 0.05);
    test1.isIndependent(data1.getVariable(x.getName()), data1.getVariable(y.getName()));
    double p1 = test1.getPValue();
    test2.isIndependent(data2.getVariable(x.getName()), data2.getVariable(z.getName()), data2.getVariable(y.getName()));
    double p2 = test2.getPValue();
    test2.isIndependent(data2.getVariable(x.getName()), data2.getVariable(z.getName()));
    double p3 = test2.getPValue();
    assertEquals(0, p1, 0.01);
    assertEquals(0, p2, 0.01);
    assertEquals(0.38, p3, 0.01);
}

Example 53 with SemPm

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

the class TestDeltaTetradTest method test3.

@Test
public void test3() {
    SemPm pm = makePm();
    DataSet data = new SemIm(pm).simulateData(1000, false);
    CovarianceMatrix cov = new CovarianceMatrix(data);
    List<Node> variables = data.getVariables();
    Node x1 = variables.get(0);
    Node x2 = variables.get(1);
    Node x3 = variables.get(2);
    Node x4 = variables.get(3);
    Node x5 = variables.get(4);
    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 test1 = new DeltaTetradTest(data);
    // DeltaTetradTest test = new DeltaTetradTest(new CorrelationMatrix(cov));
    double chiSq1 = test1.calcChiSquare(t1234, t1342);
    DeltaTetradTest test2 = new DeltaTetradTest(cov);
    // DeltaTetradTest test = new DeltaTetradTest(new CorrelationMatrix(cov));
    double chiSq2 = test2.calcChiSquare(t1234, t1342);
}

Example 54 with SemPm

use of edu.cmu.tetrad.sem.SemPm 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 55 with SemPm

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