Examples with ContinuousVariable edu.cmu.tetrad.data.ContinuousVariable used on opensource projects

Example 61 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class TestGeneralBootstrapTest method makeContinuousDAG.

private static Graph makeContinuousDAG(int numVars, int numLatentConfounders, double edgesPerNode) {
    final int numEdges = (int) (numVars * edgesPerNode);
    List<Node> vars = new ArrayList<>();
    for (int i = 0; i < numVars; i++) {
        vars.add(new ContinuousVariable(Integer.toString(i)));
    }
    return GraphUtils.randomGraph(vars, numLatentConfounders, numEdges, 30, 15, 15, false);
}

Example 62 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class TestGeneralizedSem method test3.

@Test
public void test3() {
    RandomUtil.getInstance().setSeed(49293843L);
    List<Node> variableNodes = new ArrayList<>();
    ContinuousVariable x1 = new ContinuousVariable("X1");
    ContinuousVariable x2 = new ContinuousVariable("X2");
    ContinuousVariable x3 = new ContinuousVariable("X3");
    ContinuousVariable x4 = new ContinuousVariable("X4");
    ContinuousVariable x5 = new ContinuousVariable("X5");
    variableNodes.add(x1);
    variableNodes.add(x2);
    variableNodes.add(x3);
    variableNodes.add(x4);
    variableNodes.add(x5);
    Graph _graph = new EdgeListGraph(variableNodes);
    SemGraph graph = new SemGraph(_graph);
    graph.setShowErrorTerms(true);
    Node e1 = graph.getExogenous(x1);
    Node e2 = graph.getExogenous(x2);
    Node e3 = graph.getExogenous(x3);
    Node e4 = graph.getExogenous(x4);
    Node e5 = graph.getExogenous(x5);
    graph.addDirectedEdge(x1, x3);
    graph.addDirectedEdge(x1, x2);
    graph.addDirectedEdge(x2, x3);
    graph.addDirectedEdge(x3, x4);
    graph.addDirectedEdge(x2, x4);
    graph.addDirectedEdge(x4, x5);
    graph.addDirectedEdge(x2, x5);
    graph.addDirectedEdge(x5, x1);
    GeneralizedSemPm pm = new GeneralizedSemPm(graph);
    List<Node> variablesNodes = pm.getVariableNodes();
    print(variablesNodes);
    List<Node> errorNodes = pm.getErrorNodes();
    print(errorNodes);
    try {
        pm.setNodeExpression(x1, "cos(b1) + a1 * X5 + E_X1");
        pm.setNodeExpression(x2, "a2 * X1 + E_X2");
        pm.setNodeExpression(x3, "tan(a3*X2 + a4*X1) + E_X3");
        pm.setNodeExpression(x4, "0.1 * E^X2 + X3 + E_X4");
        pm.setNodeExpression(x5, "0.1 * E^X4 + a6* X2 + E_X5");
        pm.setNodeExpression(e1, "U(0, 1)");
        pm.setNodeExpression(e2, "U(0, 1)");
        pm.setNodeExpression(e3, "U(0, 1)");
        pm.setNodeExpression(e4, "U(0, 1)");
        pm.setNodeExpression(e5, "U(0, 1)");
        GeneralizedSemIm im = new GeneralizedSemIm(pm);
        print(im);
        DataSet dataSet = im.simulateDataNSteps(1000, false);
        // System.out.println(dataSet);
        double[] d1 = dataSet.getDoubleData().getColumn(0).toArray();
        double[] d2 = dataSet.getDoubleData().getColumn(1).toArray();
        double cov = StatUtils.covariance(d1, d2);
        assertEquals(-0.002, cov, 0.001);
    } catch (ParseException e) {
        e.printStackTrace();
    }
}

Example 63 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class TestGeneralizedSem method test5.

@Test
public void test5() {
    RandomUtil.getInstance().setSeed(29999483L);
    List<Node> nodes = new ArrayList<>();
    for (int i1 = 0; i1 < 5; i1++) {
        nodes.add(new ContinuousVariable("X" + (i1 + 1)));
    }
    Graph graph = new Dag(GraphUtils.randomGraph(nodes, 0, 5, 30, 15, 15, false));
    SemPm semPm = new SemPm(graph);
    SemIm semIm = new SemIm(semPm);
    semIm.simulateDataReducedForm(1000, false);
    GeneralizedSemPm pm = new GeneralizedSemPm(semPm);
    GeneralizedSemIm im = new GeneralizedSemIm(pm, semIm);
    TetradVector e = new TetradVector(5);
    for (int i = 0; i < e.size(); i++) {
        e.set(i, RandomUtil.getInstance().nextNormal(0, 1));
    }
    TetradVector record1 = semIm.simulateOneRecord(e);
    TetradVector record2 = im.simulateOneRecord(e);
    print("XXX1" + e);
    print("XXX2" + record1);
    print("XXX3" + record2);
    for (int i = 0; i < record1.size(); i++) {
        assertEquals(record1.get(i), record2.get(i), 1e-10);
    }
}

Example 64 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class TestGeneralizedSem method test6.

@Test
public void test6() {
    RandomUtil.getInstance().setSeed(29999483L);
    int numVars = 5;
    List<Node> nodes = new ArrayList<>();
    for (int i = 0; i < numVars; i++) nodes.add(new ContinuousVariable("X" + (i + 1)));
    Graph graph = GraphUtils.randomGraphRandomForwardEdges(nodes, 0, numVars, 30, 15, 15, false, true);
    SemPm spm = new SemPm(graph);
    Parameters params = new Parameters();
    params.set("coefLow", 0.5);
    params.set("coefHigh", 1.5);
    params.set("varLow", 1);
    params.set("varHigh", 3);
    SemIm sim = new SemIm(spm, params);
    GeneralizedSemPm pm = new GeneralizedSemPm(spm);
    GeneralizedSemIm im = new GeneralizedSemIm(pm, sim);
    DataSet data = im.simulateData(1000, false);
    print(im);
    GeneralizedSemEstimator estimator = new GeneralizedSemEstimator();
    GeneralizedSemIm estIm = estimator.estimate(pm, data);
    print(estIm);
    print(estimator.getReport());
    double aSquaredStar = estimator.getaSquaredStar();
    assertEquals(1.04, aSquaredStar, 0.01);
}

Example 65 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class TestGraph method testXml.

@Test
public void testXml() {
    List<Node> nodes1 = new ArrayList<>();
    for (int i = 0; i < 10; i++) {
        nodes1.add(new ContinuousVariable("X" + (i + 1)));
    }
    Graph graph = new Dag(GraphUtils.randomGraph(nodes1, 0, 10, 30, 15, 15, false));
    Set<Triple> ambiguousTriples = new HashSet<>();
    ambiguousTriples.add(pickRandomTriple(graph));
    ambiguousTriples.add(pickRandomTriple(graph));
    graph.setAmbiguousTriples(ambiguousTriples);
    Set<Triple> underlineTriples = new HashSet<>();
    underlineTriples.add(pickRandomTriple(graph));
    underlineTriples.add(pickRandomTriple(graph));
    graph.setUnderLineTriples(underlineTriples);
    Set<Triple> dottedUnderlineTriples = new HashSet<>();
    dottedUnderlineTriples.add(pickRandomTriple(graph));
    dottedUnderlineTriples.add(pickRandomTriple(graph));
    graph.setDottedUnderLineTriples(dottedUnderlineTriples);
    Map<String, Node> nodes = new HashMap<>();
    for (Node node : graph.getNodes()) {
        nodes.put(node.getName(), node);
    }
    Element element = GraphUtils.convertToXml(graph);
    try {
        Graph _graph = GraphUtils.parseGraphXml(element, nodes);
        assertEquals(graph, new Dag(_graph));
    } catch (ParsingException e) {
        e.printStackTrace();
    }
}