Examples with SemPm edu.cmu.tetrad.sem.SemPm used on opensource projects

Example 66 with SemPm

use of edu.cmu.tetrad.sem.SemPm in project tetrad by cmu-phil.

the class TestPc method testPcStable2.

@Test
public void testPcStable2() {
    RandomUtil.getInstance().setSeed(1450030184196L);
    List<Node> nodes = new ArrayList<>();
    for (int i = 0; i < 10; i++) {
        nodes.add(new ContinuousVariable("X" + (i + 1)));
    }
    Graph graph = GraphUtils.randomGraph(nodes, 0, 10, 30, 15, 15, false);
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(200, false);
    TetradLogger.getInstance().setForceLog(false);
    IndependenceTest test = new IndTestFisherZ(data, 0.05);
    PcStableMax pc = new PcStableMax(test);
    pc.setVerbose(false);
    Graph pattern = pc.search();
    for (int i = 0; i < 1; i++) {
        DataSet data2 = DataUtils.reorderColumns(data);
        IndependenceTest test2 = new IndTestFisherZ(data2, 0.05);
        PcStableMax pc2 = new PcStableMax(test2);
        pc2.setVerbose(false);
        Graph pattern2 = pc2.search();
        assertTrue(pattern.equals(pattern2));
    }
}

Example 67 with SemPm

use of edu.cmu.tetrad.sem.SemPm in project tetrad by cmu-phil.

the class TestHistogram method testHistogram.

@Test
public void testHistogram() {
    RandomUtil.getInstance().setSeed(4829384L);
    List<Node> nodes = new ArrayList<>();
    for (int i = 0; i < 5; i++) {
        nodes.add(new ContinuousVariable("X" + (i + 1)));
    }
    Dag trueGraph = new Dag(GraphUtils.randomGraph(nodes, 0, 5, 30, 15, 15, false));
    int sampleSize = 1000;
    // Continuous
    SemPm semPm = new SemPm(trueGraph);
    SemIm semIm = new SemIm(semPm);
    DataSet data = semIm.simulateData(sampleSize, false);
    Histogram histogram = new Histogram(data);
    histogram.setTarget("X1");
    histogram.setNumBins(20);
    assertEquals(3.76, histogram.getMax(), 0.01);
    assertEquals(-3.83, histogram.getMin(), 0.01);
    assertEquals(1000, histogram.getN());
    histogram.setTarget("X1");
    histogram.setNumBins(10);
    histogram.addConditioningVariable("X3", 0, 1);
    histogram.addConditioningVariable("X4", 0, 1);
    histogram.removeConditioningVariable("X3");
    assertEquals(3.76, histogram.getMax(), 0.01);
    assertEquals(-3.83, histogram.getMin(), 0.01);
    assertEquals(188, histogram.getN());
    double[] arr = histogram.getContinuousData("X2");
    histogram.addConditioningVariable("X2", StatUtils.min(arr), StatUtils.mean(arr));
    // Discrete
    BayesPm bayesPm = new BayesPm(trueGraph);
    BayesIm bayesIm = new MlBayesIm(bayesPm, MlBayesIm.RANDOM);
    DataSet data2 = bayesIm.simulateData(sampleSize, false);
    // For some reason these are giving different
    // values when all of the unit tests are run are
    // once. TODO They produce stable values when
    // this particular test is run repeatedly.
    Histogram histogram2 = new Histogram(data2);
    histogram2.setTarget("X1");
    int[] frequencies1 = histogram2.getFrequencies();
    // assertEquals(928, frequencies1[0]);
    // assertEquals(72, frequencies1[1]);
    histogram2.setTarget("X1");
    histogram2.addConditioningVariable("X2", 0);
    histogram2.addConditioningVariable("X3", 1);
    int[] frequencies = histogram2.getFrequencies();
// assertEquals(377, frequencies[0]);
// assertEquals(28, frequencies[1]);
}

Example 68 with SemPm

use of edu.cmu.tetrad.sem.SemPm in project tetrad by cmu-phil.

the class TestIndTestFisherGeneralizedInverse method testDirections.

@Test
public void testDirections() {
    RandomUtil.getInstance().setSeed(48285934L);
    Graph graph1 = new EdgeListGraph();
    Graph graph2 = new EdgeListGraph();
    Node x = new GraphNode("X");
    Node y = new GraphNode("Y");
    Node z = new GraphNode("Z");
    graph1.addNode(x);
    graph1.addNode(y);
    graph1.addNode(z);
    graph2.addNode(x);
    graph2.addNode(y);
    graph2.addNode(z);
    graph1.addEdge(Edges.directedEdge(x, y));
    graph1.addEdge(Edges.directedEdge(y, z));
    graph2.addEdge(Edges.directedEdge(x, y));
    graph2.addEdge(Edges.directedEdge(z, y));
    SemPm pm1 = new SemPm(graph1);
    SemPm pm2 = new SemPm(graph2);
    SemIm im1 = new SemIm(pm1);
    SemIm im2 = new SemIm(pm2);
    im2.setEdgeCoef(x, y, im1.getEdgeCoef(x, y));
    im2.setEdgeCoef(z, y, im1.getEdgeCoef(y, z));
    DataSet data1 = im1.simulateData(500, false);
    DataSet data2 = im2.simulateData(500, false);
    IndependenceTest test1 = new IndTestFisherZGeneralizedInverse(data1, 0.05);
    IndependenceTest test2 = new IndTestFisherZGeneralizedInverse(data2, 0.05);
    test1.isIndependent(data1.getVariable(x.getName()), data1.getVariable(y.getName()));
    double p1 = test1.getPValue();
    test2.isIndependent(data2.getVariable(x.getName()), data2.getVariable(z.getName()), data2.getVariable(y.getName()));
    double p2 = test2.getPValue();
    test2.isIndependent(data2.getVariable(x.getName()), data2.getVariable(z.getName()));
    double p3 = test2.getPValue();
    assertEquals(0, p1, 0.01);
    assertEquals(0, p2, 0.01);
    assertEquals(0.38, p3, 0.01);
}

Example 69 with SemPm

use of edu.cmu.tetrad.sem.SemPm in project tetrad by cmu-phil.

the class TestRegression method setUp.

public void setUp() {
    List<Node> nodes = new ArrayList<>();
    for (int i = 0; i < 5; i++) {
        nodes.add(new GraphNode("X" + (i + 1)));
    }
    RandomUtil.getInstance().setSeed(342233L);
    Graph graph = new Dag(GraphUtils.randomGraphRandomForwardEdges(nodes, 0, 5, 3, 3, 3, false, true));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    data = im.simulateDataReducedForm(1000, false);
}

Example 70 with SemPm

use of edu.cmu.tetrad.sem.SemPm in project tetrad by cmu-phil.

the class TestSearchGraph method rtestDSeparation4.

public void rtestDSeparation4() {
    List<Node> nodes = new ArrayList<>();
    for (int i = 0; i < 100; i++) {
        nodes.add(new ContinuousVariable("X" + (i + 1)));
    }
    Graph graph = new Dag(GraphUtils.randomGraph(nodes, 20, 100, 5, 5, 5, false));
    long start, stop;
    int depth = -1;
    IndependenceTest test = new IndTestDSep(graph);
    Rfci fci = new Rfci(test);
    Fas fas = new Fas(test);
    start = System.currentTimeMillis();
    fci.setDepth(depth);
    fci.setVerbose(false);
    fci.search(fas, fas.getNodes());
    stop = System.currentTimeMillis();
    System.out.println("DSEP RFCI");
    System.out.println("# dsep checks = " + fas.getNumIndependenceTests());
    System.out.println("Elapsed " + (stop - start));
    System.out.println("Per " + fas.getNumIndependenceTests() / (double) (stop - start));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(1000, false);
    IndependenceTest test2 = new IndTestFisherZ(data, 0.001);
    Rfci fci3 = new Rfci(test2);
    Fas fas2 = new Fas(test2);
    start = System.currentTimeMillis();
    fci3.setDepth(depth);
    fci3.search(fas2, fas2.getNodes());
    stop = System.currentTimeMillis();
    System.out.println("FISHER Z RFCI");
    System.out.println("# indep checks = " + fas.getNumIndependenceTests());
    System.out.println("Elapsed " + (stop - start));
    System.out.println("Per " + fas.getNumIndependenceTests() / (double) (stop - start));
}