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

Example 1 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph 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 2 with EdgeListGraph

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

the class TestDM method test2.

@Test
public void test2() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(8);
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X2"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X2"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X4"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X4"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X5"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X5"), new ContinuousVariable("X7"));
    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, 4, 5 });
    search.setOutputs(new int[] { 2, 3, 6, 7 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    Graph foundGraph = search.search();
    print("Test Case 2");
    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("X6"));
    trueGraph.addNode(new ContinuousVariable("X7"));
    trueGraph.addNode(new ContinuousVariable("L0"));
    trueGraph.addNode(new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X3"));
    // trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X4"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X5"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L1"), new ContinuousVariable("X6"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L1"), new ContinuousVariable("X7"));
    assertTrue(foundGraph.equals(trueGraph));
}

Example 3 with EdgeListGraph

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

the class GlassoRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
public void execute() {
    Object dataModel = getDataModel();
    Parameters params = getParams();
    if (dataModel instanceof DataSet) {
        DataSet dataSet = (DataSet) dataModel;
        DoubleMatrix2D cov = new DenseDoubleMatrix2D(dataSet.getCovarianceMatrix().toArray());
        Glasso glasso = new Glasso(cov);
        glasso.setMaxit((int) params.get("maxit", 10000));
        glasso.setIa(params.getBoolean("ia", false));
        glasso.setIs(params.getBoolean("is", false));
        glasso.setItr(params.getBoolean("itr", false));
        glasso.setIpen(params.getBoolean("ipen", false));
        glasso.setThr(params.getDouble("thr", 1e-4));
        glasso.setRhoAllEqual(1.0);
        Glasso.Result result = glasso.search();
        TetradMatrix wwi = new TetradMatrix(result.getWwi().toArray());
        List<Node> variables = dataSet.getVariables();
        Graph resultGraph = new EdgeListGraph(variables);
        for (int i = 0; i < variables.size(); i++) {
            for (int j = i + 1; j < variables.size(); j++) {
                if (wwi.get(i, j) != 0.0 && wwi.get(i, j) != 0.0) {
                    resultGraph.addUndirectedEdge(variables.get(i), variables.get(j));
                }
            }
        }
        setResultGraph(resultGraph);
    }
}

Example 4 with EdgeListGraph

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

the class LoadContinuousDataSmithSim method readGraph.

public Graph readGraph(File file) {
    try {
        DataReader reader = new DataReader();
        reader.setVariablesSupplied(false);
        reader.setDelimiter(DelimiterType.COMMA);
        DataSet data = reader.parseTabular(file);
        List<Node> variables = data.getVariables();
        Graph graph = new EdgeListGraph(variables);
        for (int i = 0; i < variables.size(); i++) {
            for (int j = 0; j < variables.size(); j++) {
                if (i == j)
                    continue;
                if (data.getDouble(i, j) != 0) {
                    graph.addDirectedEdge(variables.get(i), variables.get(j));
                }
            }
        }
        return graph;
    } catch (IOException e) {
        throw new RuntimeException(e);
    }
}

Example 5 with EdgeListGraph

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

the class WGfci method search.

public Graph search() {
    test.setAlpha(alpha);
    Graph g = gfci.search();
    Graph out = new EdgeListGraph(searchVariables);
    for (int i = 0; i < searchVariables.size(); i++) {
        for (int j = i + 1; j < searchVariables.size(); j++) {
            Node x = searchVariables.get(i);
            Node y = searchVariables.get(j);
            List<Node> xNodes = variablesPerNode.get(x);
            List<Node> yNodes = variablesPerNode.get(y);
            int left = 0;
            int right = 0;
            int total = 0;
            for (int k = 0; k < xNodes.size(); k++) {
                for (int l = 0; l < yNodes.size(); l++) {
                    Edge e = g.getEdge(xNodes.get(k), yNodes.get(l));
                    if (e != null) {
                        total++;
                        if (e.pointsTowards(xNodes.get(k)))
                            left++;
                        if (e.pointsTowards(yNodes.get(l)))
                            right++;
                    }
                }
            }
            if (total > 0) {
                if (left == total)
                    out.addDirectedEdge(y, x);
                else if (right == total)
                    out.addDirectedEdge(x, y);
                else
                    out.addUndirectedEdge(x, y);
            }
        }
    }
    return out;
}