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

Example 26 with GraphNode

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

the class TestFruchtermanReingoldLayout method testLayout.

@Test
public void testLayout() {
    // Dag dag = DataGraphUtils.createRandomDag(40, 0, 80, 6, 6, 6, true);
    Dag dag = new Dag();
    GraphNode x1 = new GraphNode("X1");
    GraphNode x2 = new GraphNode("X2");
    GraphNode x3 = new GraphNode("X3");
    GraphNode x4 = new GraphNode("X4");
    GraphNode x5 = new GraphNode("X5");
    GraphNode x6 = new GraphNode("X6");
    GraphNode x7 = new GraphNode("X7");
    dag.addNode(x1);
    dag.addNode(x2);
    dag.addNode(x3);
    dag.addNode(x4);
    dag.addNode(x5);
    dag.addNode(x6);
    dag.addNode(x7);
    dag.addDirectedEdge(x1, x2);
    dag.addDirectedEdge(x2, x3);
    dag.addDirectedEdge(x4, x5);
    dag.addDirectedEdge(x5, x6);
    Dag dag2 = new Dag(dag);
    GraphUtils.circleLayout(dag, 200, 200, 150);
    FruchtermanReingoldLayout layout = new FruchtermanReingoldLayout(dag);
    layout.doLayout();
    assertEquals(dag, dag2);
}

Example 27 with GraphNode

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

the class TestUpdatedBayesIm method testCompound.

@Test
public void testCompound() {
    Node x0Node = new GraphNode("X0");
    Node x1Node = new GraphNode("X1");
    Node x2Node = new GraphNode("X2");
    Node x3Node = new GraphNode("X3");
    Node x4Node = new GraphNode("X4");
    Dag graph = new Dag();
    graph.addNode(x0Node);
    graph.addNode(x1Node);
    graph.addNode(x2Node);
    graph.addNode(x3Node);
    graph.addNode(x4Node);
    graph.addDirectedEdge(x0Node, x1Node);
    graph.addDirectedEdge(x0Node, x2Node);
    graph.addDirectedEdge(x1Node, x3Node);
    graph.addDirectedEdge(x2Node, x3Node);
    graph.addDirectedEdge(x4Node, x0Node);
    graph.addDirectedEdge(x4Node, x2Node);
    BayesPm bayesPm = new BayesPm(graph);
    MlBayesIm bayesIm = new MlBayesIm(bayesPm, MlBayesIm.RANDOM);
    UpdatedBayesIm updatedIm1 = new UpdatedBayesIm(bayesIm);
    assertEquals(bayesIm, updatedIm1);
    for (int i = 0; i < 5; i++) {
        for (int j = 0; j < 5; j++) {
            Evidence evidence1 = updatedIm1.getEvidence();
            evidence1.getProposition().disallowComplement(i, 0);
            UpdatedBayesIm updatedIm2 = new UpdatedBayesIm(updatedIm1, evidence1);
            Evidence evidence2 = updatedIm2.getEvidence();
            evidence2.getProposition().setToTautology();
            evidence2.getProposition().disallowComplement(j, 0);
            CptInvariantMarginalCalculator marginals1 = new CptInvariantMarginalCalculator(updatedIm2, evidence2);
            double marginal1 = marginals1.getMarginal(0, 0);
            Evidence evidence3 = updatedIm1.getEvidence();
            evidence3.getProposition().disallowComplement(i, 0);
            evidence3.getProposition().disallowComplement(j, 0);
            CptInvariantMarginalCalculator marginals2 = new CptInvariantMarginalCalculator(updatedIm1, evidence3);
            double marginal2 = marginals2.getMarginal(0, 0);
            assertEquals(marginal1, marginal2, 1.0e-2);
        }
    }
}

Example 28 with GraphNode

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

the class TestRowSummingUpdater method testUpdate4.

public void testUpdate4() {
    Node x0Node = new GraphNode("X0");
    Node x1Node = new GraphNode("X1");
    Node x2Node = new GraphNode("X2");
    Node x3Node = new GraphNode("X3");
    Dag graph = new Dag();
    graph.addNode(x0Node);
    graph.addNode(x1Node);
    graph.addNode(x2Node);
    graph.addNode(x3Node);
    graph.addDirectedEdge(x0Node, x1Node);
    graph.addDirectedEdge(x0Node, x2Node);
    graph.addDirectedEdge(x1Node, x3Node);
    graph.addDirectedEdge(x2Node, x3Node);
    BayesPm bayesPm = new BayesPm(graph);
    MlBayesIm bayesIm = new MlBayesIm(bayesPm, MlBayesIm.RANDOM);
    // int x0 = bayesIm.getNodeIndex(x0Node);
    // int x1 = bayesIm.getNodeIndex(x1Node);
    int x2 = bayesIm.getNodeIndex(x2Node);
    int x3 = bayesIm.getNodeIndex(x3Node);
    Evidence evidence = Evidence.tautology(bayesIm);
    evidence.getProposition().setCategory(x2, 0);
    BayesUpdater updater1 = new CptInvariantUpdater(bayesIm);
    updater1.setEvidence(evidence);
    BayesUpdater updater2 = new RowSummingExactUpdater(bayesIm);
    updater2.setEvidence(evidence);
    double marginal1 = updater1.getMarginal(x3, 0);
    double marginal2 = updater2.getMarginal(x3, 0);
    assertEquals(marginal1, marginal2, 0.000001);
}

Example 29 with GraphNode

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

the class TestRowSummingUpdater method sampleBayesIm0.

private BayesIm sampleBayesIm0() {
    Node z = new GraphNode("z");
    Dag graph = new Dag();
    graph.addNode(z);
    BayesPm bayesPm = new BayesPm(graph);
    BayesIm bayesIm1 = new MlBayesIm(bayesPm);
    bayesIm1.setProbability(0, 0, 0, .3);
    bayesIm1.setProbability(0, 0, 1, .7);
    return bayesIm1;
}

Example 30 with GraphNode

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

the class TestRowSummingUpdater method sampleBayesIm1.

private BayesIm sampleBayesIm1() {
    Node x = new GraphNode("x");
    Node z = new GraphNode("z");
    Dag graph = new Dag();
    graph.addNode(x);
    graph.addNode(z);
    graph.addDirectedEdge(x, z);
    BayesPm bayesPm = new BayesPm(graph);
    BayesIm bayesIm1 = new MlBayesIm(bayesPm);
    bayesIm1.setProbability(0, 0, 0, .3);
    bayesIm1.setProbability(0, 0, 1, .7);
    bayesIm1.setProbability(1, 0, 0, .8);
    bayesIm1.setProbability(1, 0, 1, .2);
    bayesIm1.setProbability(1, 1, 0, .4);
    bayesIm1.setProbability(1, 1, 1, .6);
    return bayesIm1;
}