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

Example 26 with EdgeListGraph

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

the class Glasso method search.

public Graph search(DataModel ds, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        DoubleMatrix2D cov = new DenseDoubleMatrix2D(DataUtils.getContinuousDataSet(ds).getCovarianceMatrix().toArray());
        edu.cmu.tetrad.search.Glasso glasso = new edu.cmu.tetrad.search.Glasso(cov);
        glasso.setMaxit((int) parameters.getInt("maxit"));
        glasso.setIa(parameters.getBoolean("ia"));
        glasso.setIs(parameters.getBoolean("is"));
        glasso.setItr(parameters.getBoolean("itr"));
        glasso.setIpen(parameters.getBoolean("ipen"));
        glasso.setThr(parameters.getDouble("thr"));
        glasso.setRhoAllEqual(1.0);
        edu.cmu.tetrad.search.Glasso.Result result = glasso.search();
        TetradMatrix wwi = new TetradMatrix(result.getWwi().toArray());
        List<Node> variables = ds.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));
                }
            }
        }
        return resultGraph;
    } else {
        Glasso algorithm = new Glasso();
        DataSet data = (DataSet) ds;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, algorithm, parameters.getInt("bootstrapSampleSize"));
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}

Example 27 with EdgeListGraph

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

the class MixedFgesDiscretingContinuousVariables method convertBack.

private Graph convertBack(DataSet Dk, Graph p) {
    Graph p2 = new EdgeListGraph(Dk.getVariables());
    for (int i = 0; i < p.getNodes().size(); i++) {
        for (int j = i + 1; j < p.getNodes().size(); j++) {
            Node v1 = p.getNodes().get(i);
            Node v2 = p.getNodes().get(j);
            Edge e = p.getEdge(v1, v2);
            if (e != null) {
                Node w1 = Dk.getVariable(e.getNode1().getName());
                Node w2 = Dk.getVariable(e.getNode2().getName());
                Edge e2 = new Edge(w1, w2, e.getEndpoint1(), e.getEndpoint2());
                p2.addEdge(e2);
            }
        }
    }
    return p2;
}

Example 28 with EdgeListGraph

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

the class MixedFgesTreatingDiscreteAsContinuous method convertBack.

private Graph convertBack(DataSet Dk, Graph p) {
    Graph p2 = new EdgeListGraph(Dk.getVariables());
    for (int i = 0; i < p.getNodes().size(); i++) {
        for (int j = i + 1; j < p.getNodes().size(); j++) {
            Node v1 = p.getNodes().get(i);
            Node v2 = p.getNodes().get(j);
            Edge e = p.getEdge(v1, v2);
            if (e != null) {
                Node w1 = Dk.getVariable(e.getNode1().getName());
                Node w2 = Dk.getVariable(e.getNode2().getName());
                Edge e2 = new Edge(w1, w2, e.getEndpoint1(), e.getEndpoint2());
                p2.addEdge(e2);
            }
        }
    }
    return p2;
}

Example 29 with EdgeListGraph

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

the class WFges method search.

public Graph search() {
    score.setPenaltyDiscount(penaltyDiscount);
    Graph g = fges.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;
}

Example 30 with EdgeListGraph

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

the class FgesDisplay method setDisplayGraph.

private void setDisplayGraph() {
    int index = getIndexable().getIndex();
    if (topGraphs.size() == 0) {
        workbench.setGraph(new EdgeListGraph());
    } else {
        ScoredGraph scoredGraph = topGraphs.get(index);
        workbench.setGraph(scoredGraph.getGraph());
    }
}