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

Example 6 with Node

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

the class SpecialGraphClark method createGraph.

@Override
public Graph createGraph(Parameters parameters) {
    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(z, x);
    // g.addDirectedEdge(z, y);
    g.addDirectedEdge(x, y);
    g.addDirectedEdge(x, z);
    g.addDirectedEdge(y, z);
    // 
    return g;
}

Example 7 with Node

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

the class TestAutisticClassification method testForBiwei.

// @Test
public void testForBiwei() {
    Parameters parameters = new Parameters();
    parameters.set("penaltyDiscount", 2);
    parameters.set("depth", -1);
    parameters.set("numRuns", 10);
    parameters.set("randomSelectionSize", 1);
    parameters.set("Structure", "Placeholder");
    FaskGraphs files = new FaskGraphs("/Users/jdramsey/Downloads/USM_ABIDE", new Parameters());
    List<DataSet> datasets = files.getDatasets();
    List<String> filenames = files.getFilenames();
    for (int i = 0; i < datasets.size(); i++) {
        DataSet dataSet = datasets.get(i);
        SemBicScore score = new SemBicScore(new CovarianceMatrixOnTheFly(dataSet));
        Fas fas = new Fas(new IndTestScore(score));
        Graph graph = fas.search();
        System.out.println(graph);
        List<Node> nodes = graph.getNodes();
        StringBuilder b = new StringBuilder();
        for (int j = 0; j < nodes.size(); j++) {
            for (int k = 0; k < nodes.size(); k++) {
                if (graph.isAdjacentTo(nodes.get(j), nodes.get(k))) {
                    b.append("1 ");
                } else {
                    b.append("0 ");
                }
            }
            b.append("\n");
        }
        try {
            File dir = new File("/Users/jdramsey/Downloads/biwei/USM_ABIDE");
            dir.mkdirs();
            File file = new File(dir, filenames.get(i) + ".graph.txt");
            PrintStream out = new PrintStream(file);
            out.println(b);
            out.close();
        } catch (FileNotFoundException e) {
            e.printStackTrace();
        }
    }
}

Example 8 with Node

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

the class TestBayesXml method sampleBayesIm3.

private static BayesIm sampleBayesIm3() {
    Node a = new GraphNode("a");
    a.setNodeType(NodeType.LATENT);
    a.setCenterX(5);
    a.setCenterY(5);
    Node b = new GraphNode("b");
    Node c = new GraphNode("c");
    Dag graph;
    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 9 with Node

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

the class TestBayesXml method sampleBayesIm1.

private static BayesIm sampleBayesIm1() {
    Node a = new GraphNode("a");
    Node b = new GraphNode("b");
    Node c = new GraphNode("c");
    Dag graph;
    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);
    BayesIm bayesIm1 = new MlBayesIm(bayesPm);
    bayesIm1.setProbability(0, 0, 0, .3);
    bayesIm1.setProbability(0, 0, 1, .7);
    bayesIm1.setProbability(1, 0, 0, .3);
    bayesIm1.setProbability(1, 0, 1, .4);
    bayesIm1.setProbability(1, 0, 2, .3);
    bayesIm1.setProbability(1, 1, 0, .6);
    bayesIm1.setProbability(1, 1, 1, .1);
    bayesIm1.setProbability(1, 1, 2, .3);
    bayesIm1.setProbability(2, 0, 0, .9);
    bayesIm1.setProbability(2, 0, 1, .1);
    bayesIm1.setProbability(2, 1, 0, .1);
    bayesIm1.setProbability(2, 1, 1, .9);
    bayesIm1.setProbability(2, 2, 0, .5);
    bayesIm1.setProbability(2, 2, 1, .5);
    bayesIm1.setProbability(2, 3, 0, .2);
    bayesIm1.setProbability(2, 3, 1, .8);
    bayesIm1.setProbability(2, 4, 0, .6);
    bayesIm1.setProbability(2, 4, 1, .4);
    bayesIm1.setProbability(2, 5, 0, .7);
    bayesIm1.setProbability(2, 5, 1, .3);
    return bayesIm1;
}

Example 10 with Node

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

the class TestCellProbabilities method testCreateRandom.

@Test
public void testCreateRandom() {
    RandomUtil.getInstance().setSeed(4828385834L);
    DiscreteVariable x = new DiscreteVariable("X", 3);
    DiscreteVariable y = new DiscreteVariable("Y", 3);
    DiscreteVariable z = new DiscreteVariable("Z", 3);
    DiscreteVariable w = new DiscreteVariable("W", 2);
    List<Node> variables = new LinkedList<>();
    variables.add(x);
    variables.add(y);
    variables.add(z);
    variables.add(w);
    StoredCellProbs cellProbabilities = StoredCellProbs.createRandomCellTable(variables);
    double prob = cellProbabilities.getCellProb(new int[] { 0, 0, 0, 0 });
    assertEquals(0.002, prob, 0.0001);
}