Examples with EdgeListGraph edu.cmu.tetrad.graph.EdgeListGraph used on opensource projects

Example 36 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class TestModelGenerator method testGenerate.

@Test
public void testGenerate() {
    Node x1 = new GraphNode("x1");
    Node x2 = new GraphNode("x2");
    Node x3 = new GraphNode("x3");
    Node x4 = new GraphNode("x4");
    Node x5 = new GraphNode("x5");
    // graph = new EdgeListGraph();
    Graph graph = new EdgeListGraph();
    graph.clear();
    // Add and remove some nodes.
    graph.addNode(x1);
    graph.addNode(x2);
    graph.addNode(x3);
    graph.addNode(x4);
    graph.addNode(x5);
    graph.addDirectedEdge(x1, x2);
    graph.addDirectedEdge(x2, x3);
    graph.addDirectedEdge(x3, x4);
    List<Graph> variants1 = ModelGenerator.generate(graph);
    assertEquals(17, variants1.size());
}

Example 37 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class TestSemProposition method constructGraph1.

private Graph constructGraph1() {
    Graph graph = new EdgeListGraph();
    Node x1 = new GraphNode("X1");
    Node x2 = new GraphNode("X2");
    Node x3 = new GraphNode("X3");
    Node x4 = new GraphNode("X4");
    Node x5 = new GraphNode("X5");
    graph.addNode(x1);
    graph.addNode(x2);
    graph.addNode(x3);
    graph.addNode(x4);
    graph.addNode(x5);
    graph.addDirectedEdge(x1, x2);
    graph.addDirectedEdge(x2, x3);
    graph.addDirectedEdge(x3, x4);
    graph.addDirectedEdge(x1, x4);
    graph.addDirectedEdge(x4, x5);
    return graph;
}

Example 38 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class TestSimulatedFmri method testClark2.

// @Test
public void testClark2() {
    Node x = new ContinuousVariable("X");
    Node y = new ContinuousVariable("Y");
    Node z = new ContinuousVariable("Z");
    Graph g = new EdgeListGraph();
    g.addNode(x);
    g.addNode(y);
    g.addNode(z);
    g.addDirectedEdge(x, y);
    g.addDirectedEdge(x, z);
    g.addDirectedEdge(y, z);
    GeneralizedSemPm pm = new GeneralizedSemPm(g);
    try {
        pm.setNodeExpression(g.getNode("X"), "E_X");
        pm.setNodeExpression(g.getNode("Y"), "0.4 * X + E_Y");
        pm.setNodeExpression(g.getNode("Z"), "0.4 * X + 0.4 * Y + E_Z");
        String error = "pow(Uniform(0, 1), 1.5)";
        pm.setNodeExpression(pm.getErrorNode(g.getNode("X")), error);
        pm.setNodeExpression(pm.getErrorNode(g.getNode("Y")), error);
        pm.setNodeExpression(pm.getErrorNode(g.getNode("Z")), error);
    } catch (ParseException e) {
        System.out.println(e);
    }
    GeneralizedSemIm im = new GeneralizedSemIm(pm);
    DataSet data = im.simulateData(1000, false);
    edu.cmu.tetrad.search.SemBicScore score = new edu.cmu.tetrad.search.SemBicScore(new CovarianceMatrixOnTheFly(data, false));
    Fask fask = new Fask(data, score);
    fask.setPenaltyDiscount(1);
    fask.setAlpha(0.5);
    Graph out = fask.search();
    System.out.println(out);
}

Example 39 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class InverseCorrelation method search.

public Graph search() {
    CovarianceMatrix cov = new CovarianceMatrix(data);
    TetradMatrix _data = cov.getMatrix();
    TetradMatrix inverse = _data.inverse();
    System.out.println(inverse);
    Graph graph = new EdgeListGraph(data.getVariables());
    for (int i = 0; i < inverse.rows(); i++) {
        for (int j = i + 1; j < inverse.columns(); j++) {
            double a = inverse.get(i, j);
            double b = inverse.get(i, i);
            double c = inverse.get(j, j);
            double r = -a / Math.sqrt(b * c);
            int sampleSize = data.getNumRows();
            int z = data.getNumColumns();
            double fisherZ = Math.sqrt(sampleSize - z - 3.0) * 0.5 * (Math.log(1.0 + r) - Math.log(1.0 - r));
            double p = getPValue(fisherZ);
            if (p < threshold) {
                Node x = graph.getNodes().get(i);
                Node y = graph.getNodes().get(j);
                graph.addUndirectedEdge(x, y);
            }
        // if (abs(fisherZ) > threshold) {
        // System.out.println(fisherZ + " &&& " + p);
        // Node x = graph.getNodes().get(i);
        // Node y = graph.getNodes().get(j);
        // graph.addUndirectedEdge(x, y);
        // }
        // if (Math.abs(inverse.get(i, j)) > threshold) {
        // Node x = graph.getNodes().get(i);
        // Node y = graph.getNodes().get(j);
        // graph.addUndirectedEdge(x, y);
        // }
        }
    }
    return graph;
}

Example 40 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class TestDM method test5.

// Three latent collider case
@Test
public void test5() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(6);
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X4"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X4"));
    graph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("X4"));
    graph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("X5"));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(100000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1, 2 });
    search.setOutputs(new int[] { 3, 4, 5 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    Graph foundGraph = search.search();
    print("Three Latent Collider Case");
    Graph trueGraph = new EdgeListGraph();
    trueGraph.addNode(new ContinuousVariable("X0"));
    trueGraph.addNode(new ContinuousVariable("X1"));
    trueGraph.addNode(new ContinuousVariable("X2"));
    trueGraph.addNode(new ContinuousVariable("X3"));
    trueGraph.addNode(new ContinuousVariable("X4"));
    trueGraph.addNode(new ContinuousVariable("X5"));
    trueGraph.addNode(new ContinuousVariable("L0"));
    trueGraph.addNode(new ContinuousVariable("L1"));
    trueGraph.addNode(new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L1"), new ContinuousVariable("X4"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L2"), new ContinuousVariable("X5"));
    assertTrue(foundGraph.equals(trueGraph));
}