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

Example 51 with Dag

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

the class TestCptInvariantUpdater method testUpdate5.

@Test
public void testUpdate5() {
    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);
    int x1 = bayesIm.getNodeIndex(x1Node);
    int x2 = bayesIm.getNodeIndex(x2Node);
    int x3 = bayesIm.getNodeIndex(x3Node);
    Evidence evidence = Evidence.tautology(bayesIm);
    evidence.getProposition().setCategory(x1, 1);
    evidence.getProposition().setCategory(x2, 0);
    evidence.getNodeIndex("X1");
    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 52 with Dag

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

the class TestBayesXml method sampleBayesIm2.

private static BayesIm sampleBayesIm2() {
    Node a = new GraphNode("a");
    Node b = new GraphNode("b");
    Node c = new GraphNode("c");
    Dag graph = new Dag();
    graph.addNode(a);
    graph.addNode(b);
    graph.addNode(c);
    graph.addDirectedEdge(a, b);
    graph.addDirectedEdge(a, c);
    graph.addDirectedEdge(b, c);
    BayesPm bayesPm = new BayesPm(graph);
    bayesPm.setNumCategories(b, 3);
    return new MlBayesIm(bayesPm, MlBayesIm.RANDOM);
}

Example 53 with Dag

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

the class TestDagScorer method test1.

@Test
public void test1() {
    RandomUtil.getInstance().setSeed(492839483L);
    List<Node> nodes = new ArrayList<>();
    for (int i = 0; i < 10; i++) {
        nodes.add(new ContinuousVariable("X" + (i + 1)));
    }
    Graph dag = new Dag(GraphUtils.randomGraph(nodes, 0, 10, 30, 15, 15, false));
    SemPm pm = new SemPm(dag);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(1000, false);
    GraphUtils.replaceNodes(dag, data.getVariables());
    SemEstimator est = new SemEstimator(data, pm);
    SemIm estSem = est.estimate();
    double fml = estSem.getScore();
    assertEquals(0.0369, fml, 0.001);
    dag = GraphUtils.replaceNodes(dag, data.getVariables());
    Scorer scorer = new DagScorer(data);
    double _fml = scorer.score(dag);
    assertEquals(0.0358, _fml, 0.001);
    double bicScore = scorer.getBicScore();
    assertEquals(-205, bicScore, 1);
    int dof = scorer.getDof();
    assertEquals(35, dof);
    int numFreeParams = scorer.getNumFreeParams();
    assertEquals(20, numFreeParams);
}