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

Example 1 with GeneralBootstrapTest

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

the class Cfci method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        edu.cmu.tetrad.search.Cfci search = new edu.cmu.tetrad.search.Cfci(test.getTest(dataSet, parameters));
        search.setKnowledge(knowledge);
        search.setCompleteRuleSetUsed(parameters.getBoolean("completeRuleSetUsed"));
        search.setDepth(parameters.getInt("depth"));
        return search.search();
    } else {
        Cfci algorithm = new Cfci(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 2 with GeneralBootstrapTest

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

the class Gfci method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        GFci search = new GFci(test.getTest(dataSet, parameters), score.getScore(dataSet, parameters));
        search.setMaxDegree(parameters.getInt("maxDegree"));
        search.setKnowledge(knowledge);
        search.setVerbose(parameters.getBoolean("verbose"));
        search.setFaithfulnessAssumed(parameters.getBoolean("faithfulnessAssumed"));
        search.setMaxPathLength(parameters.getInt("maxPathLength"));
        search.setCompleteRuleSetUsed(parameters.getBoolean("completeRuleSetUsed"));
        Object obj = parameters.get("printStream");
        if (obj instanceof PrintStream) {
            search.setOut((PrintStream) obj);
        }
        return search.search();
    } else {
        Gfci algorithm = new Gfci(test, score);
        // 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 3 with GeneralBootstrapTest

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

the class TsFci method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        edu.cmu.tetrad.search.TsFci search = new edu.cmu.tetrad.search.TsFci(test.getTest(dataSet, parameters));
        search.setDepth(parameters.getInt("depth"));
        search.setKnowledge(dataSet.getKnowledge());
        return search.search();
    } else {
        TsFci tsFci = new TsFci(test, algorithm);
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, tsFci, 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 4 with GeneralBootstrapTest

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

the class CpcStable method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        Graph init = null;
        if (algorithm != null) {
        // init = algorithm.search(dataSet, parameters);
        }
        edu.cmu.tetrad.search.PcAll search = new edu.cmu.tetrad.search.PcAll(test.getTest(dataSet, parameters), init);
        search.setDepth(parameters.getInt("depth"));
        search.setKnowledge(knowledge);
        search.setFasRule(PcAll.FasRule.FAS_STABLE);
        search.setColliderDiscovery(edu.cmu.tetrad.search.PcAll.ColliderDiscovery.CONSERVATIVE);
        search.setConflictRule(edu.cmu.tetrad.search.PcAll.ConflictRule.PRIORITY);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    } else {
        CpcStable cpcStable = new CpcStable(test, algorithm);
        // cpcStable.setKnowledge(knowledge);
        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 5 with GeneralBootstrapTest

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

the class Fges method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        if (algorithm != null) {
        // initialGraph = algorithm.search(dataSet, parameters);
        }
        edu.cmu.tetrad.search.Fges search = new edu.cmu.tetrad.search.Fges(score.getScore(dataSet, parameters));
        search.setFaithfulnessAssumed(parameters.getBoolean("faithfulnessAssumed"));
        search.setKnowledge(knowledge);
        search.setVerbose(parameters.getBoolean("verbose"));
        search.setMaxDegree(parameters.getInt("maxDegree"));
        search.setSymmetricFirstStep(parameters.getBoolean("symmetricFirstStep"));
        Object obj = parameters.get("printStream");
        if (obj instanceof PrintStream) {
            search.setOut((PrintStream) obj);
        }
        if (initialGraph != null) {
            search.setInitialGraph(initialGraph);
        }
        return search.search();
    } else {
        Fges fges = new Fges(score, algorithm);
        // fges.setKnowledge(knowledge);
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, fges, 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();
    }
}