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

Example 71 with SemPm

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

the class TestPcStableMax 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 72 with SemPm

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

the class GraphWithParameters method regress.

/**
 * creates a PatternWithParameters by running a regression, given a graph and data
 */
public static GraphWithParameters regress(DataSet dataSet, Graph graph) {
    SemPm semPmEstDag = new SemPm(graph);
    SemEstimator estimatorEstDag = new SemEstimator(dataSet, semPmEstDag);
    estimatorEstDag.estimate();
    SemIm semImEstDag = estimatorEstDag.getEstimatedSem();
    GraphWithParameters estimatedGraph = new GraphWithParameters(semImEstDag, graph);
    return estimatedGraph;
}

Example 73 with SemPm

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

the class TestDM method test5.

// Three latent collider case
@Test
public void test5() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(6);
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X4"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X4"));
    graph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("X4"));
    graph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("X5"));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(100000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1, 2 });
    search.setOutputs(new int[] { 3, 4, 5 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    Graph foundGraph = search.search();
    print("Three Latent Collider Case");
    Graph trueGraph = new EdgeListGraph();
    trueGraph.addNode(new ContinuousVariable("X0"));
    trueGraph.addNode(new ContinuousVariable("X1"));
    trueGraph.addNode(new ContinuousVariable("X2"));
    trueGraph.addNode(new ContinuousVariable("X3"));
    trueGraph.addNode(new ContinuousVariable("X4"));
    trueGraph.addNode(new ContinuousVariable("X5"));
    trueGraph.addNode(new ContinuousVariable("L0"));
    trueGraph.addNode(new ContinuousVariable("L1"));
    trueGraph.addNode(new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L1"), new ContinuousVariable("X4"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L2"), new ContinuousVariable("X5"));
    assertTrue(foundGraph.equals(trueGraph));
}

Example 74 with SemPm

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

the class TestDM method test4.

// Three latent fork case
@Test
public void test4() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(6);
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X4"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X5"));
    graph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("X5"));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(100000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1, 2 });
    search.setOutputs(new int[] { 3, 4, 5 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    Graph foundGraph = search.search();
    print("Three Latent Fork Case");
    Graph trueGraph = new EdgeListGraph();
    trueGraph.addNode(new ContinuousVariable("X0"));
    trueGraph.addNode(new ContinuousVariable("X1"));
    trueGraph.addNode(new ContinuousVariable("X2"));
    trueGraph.addNode(new ContinuousVariable("X3"));
    trueGraph.addNode(new ContinuousVariable("X4"));
    trueGraph.addNode(new ContinuousVariable("X5"));
    trueGraph.addNode(new ContinuousVariable("L0"));
    trueGraph.addNode(new ContinuousVariable("L1"));
    trueGraph.addNode(new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L1"), new ContinuousVariable("X4"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L2"), new ContinuousVariable("X5"));
    assertTrue(foundGraph.equals(trueGraph));
}

Example 75 with SemPm

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

the class TestDM method test6.

// Four latent case.
@Test
public void test6() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    Graph graph = emptyGraph(8);
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X4"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X5"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X5"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("X6"));
    graph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("X7"));
    graph.addDirectedEdge(new ContinuousVariable("X3"), new ContinuousVariable("X7"));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    DataSet data = im.simulateData(1000, false);
    DMSearch search = new DMSearch();
    search.setInputs(new int[] { 0, 1, 2, 3 });
    search.setOutputs(new int[] { 4, 5, 6, 7 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    Graph foundGraph = search.search();
    print("Four Latent Case");
    print("search.getDmStructure().latentStructToEdgeListGraph(search.getDmStructure())");
    Graph trueGraph = new EdgeListGraph();
    trueGraph.addNode(new ContinuousVariable("X0"));
    trueGraph.addNode(new ContinuousVariable("X1"));
    trueGraph.addNode(new ContinuousVariable("X2"));
    trueGraph.addNode(new ContinuousVariable("X3"));
    trueGraph.addNode(new ContinuousVariable("X4"));
    trueGraph.addNode(new ContinuousVariable("X5"));
    trueGraph.addNode(new ContinuousVariable("X6"));
    trueGraph.addNode(new ContinuousVariable("X7"));
    trueGraph.addNode(new ContinuousVariable("L0"));
    trueGraph.addNode(new ContinuousVariable("L1"));
    trueGraph.addNode(new ContinuousVariable("L2"));
    trueGraph.addNode(new ContinuousVariable("L3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X4"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L1"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L1"), new ContinuousVariable("X5"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("L2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L2"), new ContinuousVariable("X6"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X2"), new ContinuousVariable("L3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X3"), new ContinuousVariable("L3"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L3"), new ContinuousVariable("X7"));
    assertTrue(foundGraph.equals(trueGraph));
}