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

Example 31 with EdgeListGraph

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

the class RegressionRunner method execute.

// =================PUBLIC METHODS OVERRIDING ABSTRACT=================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    if (regressorNames.size() == 0 || targetName == null) {
        outGraph = new EdgeListGraph();
        return;
    }
    if (regressorNames.contains(targetName)) {
        outGraph = new EdgeListGraph();
        return;
    }
    Regression regression;
    Node target;
    List<Node> regressors;
    if (getDataModel() instanceof DataSet) {
        DataSet _dataSet = (DataSet) getDataModel();
        regression = new RegressionDataset(_dataSet);
        target = _dataSet.getVariable(targetName);
        regressors = new LinkedList<>();
        for (String regressorName : regressorNames) {
            regressors.add(_dataSet.getVariable(regressorName));
        }
        double alpha = params.getDouble("alpha", 0.001);
        regression.setAlpha(alpha);
        result = regression.regress(target, regressors);
        outGraph = regression.getGraph();
    } else if (getDataModel() instanceof ICovarianceMatrix) {
        ICovarianceMatrix covariances = (ICovarianceMatrix) getDataModel();
        regression = new RegressionCovariance(covariances);
        target = covariances.getVariable(targetName);
        regressors = new LinkedList<>();
        for (String regressorName : regressorNames) {
            regressors.add(covariances.getVariable(regressorName));
        }
        double alpha = params.getDouble("alpha", 0.001);
        regression.setAlpha(alpha);
        result = regression.regress(target, regressors);
        outGraph = regression.getGraph();
    }
    setResultGraph(outGraph);
}

Example 32 with EdgeListGraph

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

the class DagIterator method next.

/**
 * Successive calls to this method return successive DAGs in the pattern, in a more or less natural enumeration of
 * them in which an arbitrary undirected edge is picked, oriented one way, Meek rules applied, then a remaining
 * unoriented edge is picked, oriented one way, and so on, until a DAG is obtained, and then by backtracking the
 * other orientation of each chosen edge is tried. Nonrecursive, obviously.
 * <p>
 *
 * @return a Graph instead of a DAG because sometimes, due to faulty patterns, a cyclic graph is produced, and the
 * end-user may need to decide what to do with it. The simplest thing is to construct a DAG (Dag(graph)) and catch
 * an exception.
 */
public Graph next() {
    if (storedDag != null) {
        Graph temp = storedDag;
        storedDag = null;
        return temp;
    }
    if (decoratedGraphs.isEmpty()) {
        return null;
    }
    // If it's a DAG
    if (!decoratedGraphs.getLast().hasUndirectedEdge()) {
        // oriented right, and add a graph with that oriented left.
        while (true) {
            if (decoratedGraphs.isEmpty()) {
                return null;
            }
            DecoratedGraph graph = decoratedGraphs.removeLast();
            if (graph.hasUndirectedEdge() && !graph.wasDirectedRight()) {
                throw new IllegalStateException();
            }
            if (decoratedGraphs.isEmpty() && !graph.hasUndirectedEdge()) {
                return new EdgeListGraph(graph.getGraph());
            }
            if (graph.wasDirectedRight() && !graph.wasDirectedLeft()) {
                decoratedGraphs.add(graph);
                DecoratedGraph graph1 = graph.directLeft();
                if (graph1 == null) {
                    continue;
                }
                decoratedGraphs.add(graph1);
                break;
            }
        }
    }
    // Apply right orientations and Meek orientations until there's a DAG.
    while (decoratedGraphs.getLast().hasUndirectedEdge()) {
        DecoratedGraph graph = decoratedGraphs.getLast().directRight();
        if (graph == null) {
            continue;
        }
        decoratedGraphs.add(graph);
    }
    // Return the DAG.
    return new EdgeListGraph(decoratedGraphs.getLast().getGraph());
}

Example 33 with EdgeListGraph

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

the class TestSem method constructGraph2.

private Graph constructGraph2() {
    Graph graph = new EdgeListGraph();
    Node x1 = new GraphNode("X1");
    Node x2 = new GraphNode("X2");
    Node x3 = new GraphNode("X3");
    Node x4 = new GraphNode("X4");
    Node x5 = new GraphNode("X5");
    Node x6 = new GraphNode("X6");
    Node x7 = new GraphNode("X7");
    Node x8 = new GraphNode("X8");
    graph.addNode(x1);
    graph.addNode(x2);
    graph.addNode(x3);
    graph.addNode(x4);
    graph.addNode(x5);
    graph.addNode(x6);
    graph.addNode(x7);
    graph.addNode(x8);
    graph.addDirectedEdge(x1, x2);
    graph.addDirectedEdge(x2, x3);
    graph.addDirectedEdge(x2, x6);
    graph.addDirectedEdge(x3, x7);
    graph.addDirectedEdge(x4, x5);
    graph.addDirectedEdge(x4, x6);
    graph.addDirectedEdge(x5, x3);
    graph.addDirectedEdge(x6, x8);
    graph.addDirectedEdge(x6, x7);
    return graph;
}

Example 34 with EdgeListGraph

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

the class TestSem method constructGraph1.

private Graph constructGraph1() {
    Graph graph = new EdgeListGraph();
    Node x1 = new GraphNode("X1");
    Node x2 = new GraphNode("X2");
    Node x3 = new GraphNode("X3");
    Node x4 = new GraphNode("X4");
    Node x5 = new GraphNode("X5");
    graph.addNode(x1);
    graph.addNode(x2);
    graph.addNode(x3);
    graph.addNode(x4);
    graph.addNode(x5);
    graph.addDirectedEdge(x1, x2);
    graph.addDirectedEdge(x2, x3);
    graph.addDirectedEdge(x3, x4);
    graph.addDirectedEdge(x1, x4);
    graph.addDirectedEdge(x4, x5);
    return graph;
}

Example 35 with EdgeListGraph

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

the class TestSemUpdater method constructGraph1.

private Graph constructGraph1() {
    Graph graph = new EdgeListGraph();
    Node x1 = new GraphNode("X1");
    Node x2 = new GraphNode("X2");
    Node x3 = new GraphNode("X3");
    Node x4 = new GraphNode("X4");
    Node x5 = new GraphNode("X5");
    graph.addNode(x1);
    graph.addNode(x2);
    graph.addNode(x3);
    graph.addNode(x4);
    graph.addNode(x5);
    graph.addDirectedEdge(x1, x2);
    graph.addDirectedEdge(x2, x3);
    graph.addDirectedEdge(x3, x4);
    graph.addDirectedEdge(x1, x4);
    graph.addDirectedEdge(x4, x5);
    return graph;
}