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

Example 6 with Dag

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

the class TestCptInvariantUpdater method testUpdate4.

@Test
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 7 with Dag

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

the class TestCptInvariantUpdater 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;
}

Example 8 with Dag

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

the class TestDag method checkCopy.

private void checkCopy(Graph graph) {
    Graph graph2 = new Dag(graph);
    assertEquals(graph, graph2);
}

Example 9 with Dag

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

the class TestDataLoadersRoundtrip method testDiscreteRoundtrip.

@Test
public void testDiscreteRoundtrip() {
    setUp();
    try {
        for (int i = 0; i < 1; i++) {
            List<Node> nodes = new ArrayList<>();
            for (int j = 0; j < 5; j++) {
                nodes.add(new ContinuousVariable("X" + (j + 1)));
            }
            Graph randomGraph = new Dag(GraphUtils.randomGraph(nodes, 0, 8, 30, 15, 15, false));
            Dag dag = new Dag(randomGraph);
            BayesPm bayesPm1 = new BayesPm(dag);
            MlBayesIm bayesIm1 = new MlBayesIm(bayesPm1, MlBayesIm.RANDOM);
            DataSet dataSet = bayesIm1.simulateData(10, false);
            new File("target/test_data").mkdir();
            FileWriter fileWriter = new FileWriter("target/test_data/roundtrip.dat");
            Writer writer = new PrintWriter(fileWriter);
            DataWriter.writeRectangularData(dataSet, writer, '\t');
            writer.close();
            File file = new File("target/test_data/roundtrip.dat");
            DataReader reader = new DataReader();
            reader.setKnownVariables(dataSet.getVariables());
            DataSet _dataSet = reader.parseTabular(file);
            assertTrue(dataSet.equals(_dataSet));
        }
    } catch (IOException e) {
        e.printStackTrace();
        fail(e.getMessage());
    }
}

Example 10 with Dag

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

the class TestDataLoadersRoundtrip method testContinuousRoundtrip.

@Test
public void testContinuousRoundtrip() {
    setUp();
    try {
        List<Node> nodes = new ArrayList<>();
        for (int i = 0; i < 5; i++) {
            nodes.add(new ContinuousVariable("X" + (i + 1)));
        }
        Graph randomGraph = new Dag(GraphUtils.randomGraph(nodes, 0, 5, 30, 15, 15, false));
        SemPm semPm1 = new SemPm(randomGraph);
        SemIm semIm1 = new SemIm(semPm1);
        DataSet dataSet = semIm1.simulateData(10, false);
        FileWriter fileWriter = new FileWriter("target/test_data/roundtrip.dat");
        Writer writer = new PrintWriter(fileWriter);
        DataWriter.writeRectangularData(dataSet, writer, ',');
        writer.close();
        // 
        new File("test_data").mkdir();
        File file = new File("target/test_data/roundtrip.dat");
        DataReader reader = new DataReader();
        reader.setDelimiter(DelimiterType.COMMA);
        DataSet _dataSet = reader.parseTabular(file);
        assertTrue(dataSet.equals(_dataSet));
    } catch (IOException e) {
        e.printStackTrace();
        fail();
    }
}