Examples with GeneralBootstrapTest edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest used on opensource projects

Example 21 with GeneralBootstrapTest

use of edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest in project tetrad by cmu-phil.

the class CcdMax method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        IndependenceTest test = this.test.getTest(dataSet, parameters);
        edu.cmu.tetrad.search.CcdMax search = new edu.cmu.tetrad.search.CcdMax(test);
        search.setDoColliderOrientations(parameters.getBoolean("doColliderOrientation"));
        search.setUseHeuristic(parameters.getBoolean("useMaxPOrientationHeuristic"));
        search.setMaxPathLength(parameters.getInt("maxPOrientationMaxPathLength"));
        search.setKnowledge(knowledge);
        search.setDepth(parameters.getInt("depth"));
        search.setApplyOrientAwayFromCollider(parameters.getBoolean("applyR1"));
        search.setUseOrientTowardDConnections(parameters.getBoolean("orientTowardDConnections"));
        search.setDepth(parameters.getInt("depth"));
        return search.search();
    } else {
        CcdMax algorithm = new CcdMax(test);
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, algorithm, parameters.getInt("bootstrapSampleSize"));
        search.setKnowledge(knowledge);
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}

Example 22 with GeneralBootstrapTest

use of edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest in project tetrad by cmu-phil.

the class Rfci method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        edu.cmu.tetrad.search.Rfci search = new edu.cmu.tetrad.search.Rfci(test.getTest(dataSet, parameters));
        search.setKnowledge(knowledge);
        search.setDepth(parameters.getInt("depth"));
        search.setMaxPathLength(parameters.getInt("maxPathLength"));
        search.setCompleteRuleSetUsed(parameters.getBoolean("completeRuleSetUsed"));
        return search.search();
    } else {
        Rfci algorithm = new Rfci(test);
        // algorithm.setKnowledge(knowledge);
        // if (initialGraph != null) {
        // algorithm.setInitialGraph(initialGraph);
        // }
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, algorithm, parameters.getInt("bootstrapSampleSize"));
        search.setKnowledge(knowledge);
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}

Example 23 with GeneralBootstrapTest

use of edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest in project tetrad by cmu-phil.

the class TsGfci method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        edu.cmu.tetrad.search.TsGFci search = new edu.cmu.tetrad.search.TsGFci(test.getTest(dataSet, parameters), score.getScore(dataSet, parameters));
        IKnowledge _knowledge = dataSet.getKnowledge() != null ? dataSet.getKnowledge() : new Knowledge2();
        search.setKnowledge(dataSet.getKnowledge());
        return search.search();
    } else {
        TsGfci algorithm = new TsGfci(test, score);
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, algorithm, parameters.getInt("bootstrapSampleSize"));
        search.setKnowledge(knowledge);
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}

Example 24 with GeneralBootstrapTest

use of edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest in project tetrad by cmu-phil.

the class MixedFgesDiscretingContinuousVariables method search.

public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        Discretizer discretizer = new Discretizer(DataUtils.getContinuousDataSet(dataSet));
        List<Node> nodes = dataSet.getVariables();
        for (Node node : nodes) {
            if (node instanceof ContinuousVariable) {
                discretizer.equalIntervals(node, parameters.getInt("numCategories"));
            }
        }
        dataSet = discretizer.discretize();
        DataSet _dataSet = DataUtils.getDiscreteDataSet(dataSet);
        Fges fges = new Fges(score.getScore(_dataSet, parameters));
        Graph p = fges.search();
        return convertBack(_dataSet, p);
    } else {
        MixedFgesDiscretingContinuousVariables algorithm = new MixedFgesDiscretingContinuousVariables(score);
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, algorithm, parameters.getInt("bootstrapSampleSize"));
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}

Example 25 with GeneralBootstrapTest

use of edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest in project tetrad by cmu-phil.

the class CcdMaxConcatenated method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (!parameters.getBoolean("bootstrapping")) {
        return search(Collections.singletonList((DataModel) DataUtils.getContinuousDataSet(dataSet)), parameters);
    } else {
        CcdMaxConcatenated algorithm = new CcdMaxConcatenated(test);
        algorithm.setKnowledge(knowledge);
        List<DataSet> dataSets = Collections.singletonList(DataUtils.getContinuousDataSet(dataSet));
        GeneralBootstrapTest search = new GeneralBootstrapTest(dataSets, algorithm, parameters.getInt("bootstrapSampleSize"));
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}