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

Example 81 with ContinuousVariable

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

the class IndTestMixedMultipleTTest method expandVariable.

private List<Node> expandVariable(DataSet dataSet, Node node) {
    if (node instanceof ContinuousVariable) {
        return Collections.singletonList(node);
    }
    if (node instanceof DiscreteVariable && ((DiscreteVariable) node).getNumCategories() < 3) {
        return Collections.singletonList(node);
    }
    if (!(node instanceof DiscreteVariable)) {
        throw new IllegalArgumentException();
    }
    List<String> varCats = new ArrayList<>(((DiscreteVariable) node).getCategories());
    // first category is reference
    varCats.remove(0);
    List<Node> variables = new ArrayList<>();
    for (String cat : varCats) {
        Node newVar;
        do {
            String newVarName = node.getName() + "MULTINOM" + "." + cat;
            newVar = new DiscreteVariable(newVarName, 2);
        } while (dataSet.getVariable(newVar.getName()) != null);
        variables.add(newVar);
        dataSet.addVariable(newVar);
        int newVarIndex = dataSet.getColumn(newVar);
        int numCases = dataSet.getNumRows();
        for (int l = 0; l < numCases; l++) {
            Object dataCell = dataSet.getObject(l, dataSet.getColumn(node));
            int dataCellIndex = ((DiscreteVariable) node).getIndex(dataCell.toString());
            if (dataCellIndex == ((DiscreteVariable) node).getIndex(cat))
                dataSet.setInt(l, newVarIndex, 1);
            else
                dataSet.setInt(l, newVarIndex, 0);
        }
    }
    return variables;
}

Example 82 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable 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 83 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable 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 84 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable 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));
}

Example 85 with ContinuousVariable

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

the class TestDM method test1.

@Test
public void test1() {
    // setting seed for debug.
    RandomUtil.getInstance().setSeed(29483818483L);
    NodeEqualityMode.setEqualityMode(NodeEqualityMode.Type.NAME);
    Graph graph = emptyGraph(4);
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X2"));
    graph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("X3"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X2"));
    graph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("X3"));
    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 });
    search.setOutputs(new int[] { 2, 3 });
    search.setData(data);
    search.setTrueInputs(search.getInputs());
    Graph foundGraph = search.search();
    print("Test Case 1");
    // System.out.println(search.getDmStructure());
    // System.out.println(foundGraph);
    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("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X0"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("X1"), new ContinuousVariable("L0"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X2"));
    trueGraph.addDirectedEdge(new ContinuousVariable("L0"), new ContinuousVariable("X3"));
    assertEquals(trueGraph, foundGraph);
}