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

Example 21 with Node

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

the class ExploreAutisticsNeurotypicals method printDataTranspose.

private static void printDataTranspose(String path, String prefix, DataSet dataSet) {
    List<Node> nodes = dataSet.getVariables();
    Node group = dataSet.getVariable("Group");
    List<Node> _nodes = new ArrayList<>();
    for (int i = 0; i < nodes.size(); i++) {
        if (nodes.get(i) == group) {
            _nodes.add(group);
        } else {
            _nodes.add(new ContinuousVariable("X" + (i + 1)));
        }
    }
    TetradMatrix m = dataSet.getDoubleData();
    TetradMatrix mt = m.transpose();
    List<Node> tvars = new ArrayList<>();
    for (int i = 0; i < mt.columns(); i++) tvars.add(new ContinuousVariable("S" + (i + 1)));
    dataSet = new BoxDataSet(new DoubleDataBox(mt.toArray()), tvars);
    // dataSet = new BoxDataSet(new DoubleDataBox(dataSet.getDoubleData().toArray()), _nodes);
    dataSet.setNumberFormat(new DecimalFormat("0"));
    File file1 = new File(path, prefix + ".data.txt");
    File file2 = new File(path, prefix + ".dict.txt");
    try {
        PrintStream out1 = new PrintStream(new FileOutputStream(file1));
        PrintStream out2 = new PrintStream(new FileOutputStream(file2));
        out1.println(dataSet);
        out1.close();
        for (int i = 0; i < nodes.size(); i++) {
            out2.println(_nodes.get(i) + "\t" + nodes.get(i));
        }
        out2.println("Group");
        out2.close();
    } catch (FileNotFoundException e) {
        e.printStackTrace();
        throw new RuntimeException();
    }
}

Example 22 with Node

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

the class TestColtDataSet method testPermuteRows.

@Test
public void testPermuteRows() {
    ContinuousVariable x1 = new ContinuousVariable("X1");
    ContinuousVariable x2 = new ContinuousVariable("X2");
    List<Node> nodes = new ArrayList<>();
    nodes.add(x1);
    nodes.add(x2);
    DataSet dataSet = new ColtDataSet(3, nodes);
    RandomUtil randomUtil = RandomUtil.getInstance();
    for (int i = 0; i < 3; i++) {
        for (int j = 0; j < 2; j++) {
            dataSet.setDouble(i, j, randomUtil.nextDouble());
        }
    }
    ColtDataSet _dataSet = new ColtDataSet((ColtDataSet) dataSet);
    dataSet.permuteRows();
    I: for (int i = 0; i < dataSet.getNumRows(); i++) {
        TetradVector v = _dataSet.getDoubleData().getRow(i);
        for (int j = 0; j < dataSet.getNumRows(); j++) {
            TetradVector w = dataSet.getDoubleData().getRow(j);
            if (v.equals(w)) {
                continue I;
            }
        }
        fail("Missing row in permutation.");
    }
}

Example 23 with Node

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

the class TestColtDataSet method testContinuous.

@Test
public final void testContinuous() {
    int rows = 10;
    int cols = 5;
    List<Node> _variables = new LinkedList<>();
    for (int i = 0; i < cols; i++) {
        _variables.add(new ContinuousVariable("X" + i));
    }
    DataSet dataSet = new ColtDataSet(rows, _variables);
    RandomUtil randomUtil = RandomUtil.getInstance();
    for (int i = 0; i < rows; i++) {
        for (int j = 0; j < cols; j++) {
            dataSet.setDouble(i, j, randomUtil.nextDouble());
        }
    }
    List<Node> variables = dataSet.getVariables();
    List<Node> newVars = new LinkedList<>();
    newVars.add(variables.get(2));
    newVars.add(variables.get(4));
    DataSet _dataSet = dataSet.subsetColumns(newVars);
    assertEquals(dataSet.getDoubleData().getColumn(2).get(0), _dataSet.getDoubleData().getColumn(0).get(0), .001);
    assertEquals(dataSet.getDoubleData().getColumn(4).get(0), _dataSet.getDoubleData().getColumn(1).get(0), .001);
}

Example 24 with Node

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

the class TestColtDataSet method testRemoveRows.

@Test
public void testRemoveRows() {
    int rows = 10;
    int cols = 5;
    List<Node> variables = new LinkedList<>();
    for (int i = 0; i < cols; i++) {
        variables.add(new ContinuousVariable("X" + i));
    }
    DataSet dataSet = new ColtDataSet(rows, variables);
    RandomUtil randomUtil = RandomUtil.getInstance();
    for (int i = 0; i < rows; i++) {
        for (int j = 0; j < cols; j++) {
            dataSet.setDouble(i, j, randomUtil.nextDouble());
        }
    }
    int numRows = dataSet.getNumRows();
    double d = dataSet.getDouble(3, 0);
    int[] _rows = new int[2];
    _rows[0] = 1;
    _rows[1] = 2;
    dataSet.removeRows(_rows);
    assertEquals(numRows - 2, dataSet.getNumRows());
    assertEquals(d, dataSet.getDouble(1, 0), 0.001);
}

Example 25 with Node

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

the class TestDag method checkAddRemoveNodes.

private void checkAddRemoveNodes(Dag graph) {
    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(x5, x4);
    List<Node> children = graph.getChildren(x1);
    List<Node> parents = graph.getParents(x4);
    assertTrue(children.contains(x2));
    assertTrue(parents.contains(x3));
    assertTrue(parents.contains(x5));
    assertTrue(graph.isDConnectedTo(x1, x3, Collections.EMPTY_LIST));
    assertTrue(graph.existsDirectedPathFromTo(x1, x4));
    assertTrue(!graph.existsDirectedPathFromTo(x1, x5));
    assertTrue(graph.isAncestorOf(x2, x4));
    assertTrue(!graph.isAncestorOf(x4, x2));
    assertTrue(graph.isDescendentOf(x4, x2));
    assertTrue(!graph.isDescendentOf(x2, x4));
}