Examples with Knowledge2 edu.cmu.tetrad.data.Knowledge2 used on opensource projects

Example 16 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class FciCcdSearchEditor method layoutByKnowledge.

public void layoutByKnowledge() {
    GraphWorkbench resultWorkbench = getWorkbench();
    Graph graph = resultWorkbench.getGraph();
    IKnowledge knowledge = (IKnowledge) getAlgorithmRunner().getParams().get("knowledge", new Knowledge2());
    SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
}

Example 17 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class TestKnowledge method test1.

@Test
public final void test1() {
    List<Node> nodes1 = new ArrayList<>();
    for (int i1 = 0; i1 < 10; i1++) {
        nodes1.add(new ContinuousVariable("X" + (i1 + 1)));
    }
    Graph g = GraphUtils.randomGraph(nodes1, 0, 10, 3, 3, 3, false);
    g.getNode("X1").setName("X1.1");
    g.getNode("X2").setName("X2-1");
    List<Node> nodes = g.getNodes();
    List<String> varNames = new ArrayList<>();
    for (Node node : nodes) {
        varNames.add(node.getName());
    }
    IKnowledge knowledge = new Knowledge2(varNames);
    knowledge.addToTier(0, "X1.*1");
    knowledge.addToTier(0, "X2-1");
    knowledge.addToTier(1, "X3");
    knowledge.setForbidden("X4", "X5");
    knowledge.setRequired("X6", "X7");
    knowledge.setRequired("X7", "X8");
    assertTrue(knowledge.isForbidden("X4", "X5"));
    assertFalse(knowledge.isForbidden("X1.1", "X2-1"));
    assertTrue(knowledge.isForbidden("X3", "X2-1"));
    assertTrue(knowledge.isRequired("X6", "X7"));
    IKnowledge copy = knowledge.copy();
    assertTrue(copy.isForbidden("X4", "X5"));
    assertFalse(copy.isForbidden("X1", "X2-1"));
    assertTrue(copy.isForbidden("X3", "X2-1"));
    knowledge.setTierForbiddenWithin(0, true);
    assertTrue(knowledge.isForbidden("X1.1", "X2-1"));
    assertTrue(knowledge.isForbidden("X2-1", "X1.1"));
    assertFalse(knowledge.isForbidden("X1.1", "X1.1"));
    boolean found = false;
    for (Iterator i = knowledge.forbiddenEdgesIterator(); i.hasNext(); ) {
        KnowledgeEdge edge = (KnowledgeEdge) i.next();
        if (edge.getFrom().equals("X1.1") && edge.getTo().equals("X2-1")) {
            found = true;
        }
    }
    assertTrue(found);
    knowledge.setTierForbiddenWithin(0, false);
    assertFalse(knowledge.isForbidden("X1.1", "X2-1"));
    assertFalse(knowledge.isForbidden("X2-1", "X1.1"));
    assertFalse(knowledge.isForbidden("X1.1", "X1.1"));
}

Example 18 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class TestKnowledge method test3.

@Test
public final void test3() {
    List<String> vars = new ArrayList<>();
    final int numVars = 1000;
    for (int i = 0; i < numVars; i++) {
        vars.add("X" + i);
    }
    IKnowledge knowledge = new Knowledge2(vars);
    knowledge.setForbidden("X1*", "X2*");
    knowledge.setForbidden("X3*", "X4*");
    knowledge.setForbidden("X5*", "X6*");
    knowledge.addToTier(0, "X7*");
    knowledge.addToTier(1, "X8*");
    knowledge.addToTier(2, "X9*");
    for (int i = 0; i < numVars; i++) {
        assertTrue(knowledge.isForbidden("X11", "X22"));
    }
}

Example 19 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class TestPcd method testSearch3.

/**
 * This will fail if the orientation loop doesn't continue after the first orientation.
 */
// @Test
public void testSearch3() {
    IKnowledge knowledge = new Knowledge2();
    knowledge.setForbidden("B", "D");
    knowledge.setForbidden("D", "B");
    checkWithKnowledge("A-->B,C-->B,B-->D", "A-->B,C-->B,D", knowledge);
}

Example 20 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class TimeLagGraphWrapper method getKnowledge.

public IKnowledge getKnowledge() {
    // need to fix this!
    int numLags = 1;
    List<Node> variables = graph.getNodes();
    List<Integer> laglist = new ArrayList<>();
    IKnowledge knowledge1 = new Knowledge2();
    int lag;
    for (Node node : variables) {
        String varName = node.getName();
        String tmp;
        if (varName.indexOf(':') == -1) {
            lag = 0;
            laglist.add(lag);
        } else {
            tmp = varName.substring(varName.indexOf(':') + 1, varName.length());
            lag = Integer.parseInt(tmp);
            laglist.add(lag);
        }
    }
    numLags = Collections.max(laglist);
    for (Node node : variables) {
        String varName = node.getName();
        String tmp;
        if (varName.indexOf(':') == -1) {
            lag = 0;
            laglist.add(lag);
        } else {
            tmp = varName.substring(varName.indexOf(':') + 1, varName.length());
            lag = Integer.parseInt(tmp);
            laglist.add(lag);
        }
        knowledge1.addToTier(numLags - lag, node.getName());
    }
    System.out.println("Knowledge in graph = " + knowledge1);
    return knowledge1;
}