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

Example 41 with Knowledge2

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

the class IonRunner method execute.

// =================PUBLIC METHODS OVERRIDING ABSTRACT=================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    System.out.println("Executing.");
    IonJoeModifications ion = new IonJoeModifications(getGraphs());
    ion.setAdjacencySearch(getParams().getBoolean("pruneByAdjacencies", true));
    ion.setPathLengthSearch(getParams().getBoolean("pruneByPathLength", true));
    ion.setKnowledge((IKnowledge) getParams().get("knowledge", new Knowledge2()));
    List<Graph> graphs = ion.search();
    Collections.sort(graphs, new Comparator<Graph>() {

        public int compare(Graph graph, Graph graph1) {
            return graph.getNumEdges() - graph1.getNumEdges();
        }
    });
    if (graphs == null) {
        throw new NullPointerException();
    }
    if (!graphs.isEmpty()) {
        setResultGraph(graphs.get(0));
    }
    System.out.println("graphs = " + graphs);
    getParams().set("graphIndex", 0);
    this.graphs = graphs;
}

Example 42 with Knowledge2

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

the class KpcRunner method getMeekRules.

public ImpliedOrientation getMeekRules() {
    MeekRules rules = new MeekRules();
    rules.setAggressivelyPreventCycles(this.isAggressivelyPreventCycles());
    rules.setKnowledge((IKnowledge) getParams().get("knowledge", new Knowledge2()));
    return rules;
}

Example 43 with Knowledge2

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

the class MbFanSearchRunner method execute.

// =================PUBLIC METHODS OVERRIDING ABSTRACT=================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    int pcDepth = getParams().getInt("depth", -1);
    Mbfs mbfs = new Mbfs(getIndependenceTest(), pcDepth);
    Parameters params = getParams();
    if (params instanceof Parameters) {
        mbfs.setAggressivelyPreventCycles(params.getBoolean("aggressivelyPreventCycles", false));
    }
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    mbfs.setKnowledge(knowledge);
    String targetName = getParams().getString("targetName", null);
    Graph graph = mbfs.search(targetName);
    setResultGraph(graph);
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else if (knowledge.isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    this.mbfs = mbfs;
}

Example 44 with Knowledge2

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

the class MbfsRunner method execute.

// =================PUBLIC METHODS OVERRIDING ABSTRACT=================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    // int pcDepth = ((Parameters) getParameters()).getMaxIndegree();
    // Mbfs mbfs = new Mbfs(getIndependenceTest(), pcDepth);
    // Parameters params = getParameters();
    // if (params instanceof Parameters) {
    // mbfs.setAggressivelyPreventCycles(((Parameters) params)
    // .isAggressivelyPreventCycles());
    // }
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    // mbfs.setKnowledge(knowledge);
    String targetName = getParams().getString("targetName", null);
    // Graph searchGraph = mbfs.search(targetName);
    // setResultGraph(searchGraph);
    DataSet dataSet = (DataSet) getDataModelList().get(0);
    SemBicScore score = new SemBicScore(new CovarianceMatrixOnTheFly(dataSet));
    score.setPenaltyDiscount(getParams().getDouble("alpha", 0.001));
    FgesMb search = new FgesMb(score);
    search.setFaithfulnessAssumed(true);
    Graph searchGraph = search.search(dataSet.getVariable(targetName));
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(searchGraph, getSourceGraph());
    } else if (knowledge.isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(searchGraph, knowledge);
    } else {
        GraphUtils.circleLayout(searchGraph, 200, 200, 150);
    }
    // this.mbfs = mbfs;
    setResultGraph(searchGraph);
}

Example 45 with Knowledge2

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

the class MmhcRunner method getMeekRules.

public ImpliedOrientation getMeekRules() {
    MeekRules rules = new MeekRules();
    rules.setKnowledge((IKnowledge) getParams().get("knowledge", new Knowledge2()));
    return rules;
}