Examples with IndependenceTest edu.cmu.tetrad.search.IndependenceTest used on opensource projects

Example 6 with IndependenceTest

use of edu.cmu.tetrad.search.IndependenceTest in project tetrad by cmu-phil.

the class IndependenceFactsEditor method generateResults.

private void generateResults() {
    results = new ArrayList<>();
    List<String> dataVars = getDataVars();
    if (getVars().size() < 2) {
        tableModel.fireTableDataChanged();
        return;
    }
    // Need a choice generator over the ?'s, and a depth choice generator over the +'s. The +'s all have to come
    // at the end at index >= 2.
    int numQuestionMarksFirstTwo = 0;
    int numQuestionMarksRest = 0;
    int numPluses = 0;
    int numFixed = 0;
    for (int i = 0; i < vars.size(); i++) {
        String var = vars.get(i);
        if ("?".equals(var) && i < 2)
            numQuestionMarksFirstTwo++;
        else if ("?".equals(var))
            numQuestionMarksRest++;
        else if ("+".equals(var))
            numPluses++;
        else
            numFixed++;
    }
    int[] questionMarkFirstTwoIndices = new int[numQuestionMarksFirstTwo];
    int[] questionMarkRestIndices = new int[numQuestionMarksRest];
    int[] plusIndices = new int[numPluses];
    int[] fixedIndices = new int[numFixed];
    String[] fixedVars = new String[numFixed];
    int _i = -1;
    int _j = -1;
    int _k = -1;
    int _l = -1;
    for (int i = 0; i < vars.size(); i++) {
        if ("?".equals(vars.get(i)) && i < 2)
            questionMarkFirstTwoIndices[++_i] = i;
        else if ("?".equals(vars.get(i)))
            questionMarkRestIndices[++_j] = i;
        else if ("+".equals(vars.get(i)))
            plusIndices[++_k] = i;
        else {
            fixedIndices[++_l] = i;
            fixedVars[_l] = vars.get(i);
        }
    }
    List<String> vars1 = new ArrayList<>(dataVars);
    vars1.removeAll(vars);
    ChoiceGenerator gen1 = new ChoiceGenerator(vars1.size(), questionMarkFirstTwoIndices.length);
    int[] choice1;
    LOOP: while ((choice1 = gen1.next()) != null) {
        List<String> s2 = asList(choice1, vars1);
        List<String> vars2 = new ArrayList<>(vars1);
        vars2.removeAll(s2);
        ChoiceGenerator gen2 = new ChoiceGenerator(vars2.size(), questionMarkRestIndices.length);
        int[] choice2;
        while ((choice2 = gen2.next()) != null) {
            List<String> s3 = asList(choice2, vars2);
            List<String> vars3 = new ArrayList<>(vars2);
            vars3.removeAll(s3);
            DepthChoiceGenerator gen3 = new DepthChoiceGenerator(vars3.size(), plusIndices.length);
            int[] choice3;
            while ((choice3 = gen3.next()) != null) {
                results.add(new ArrayList<IndependenceResult>());
                for (int prod = 0; prod < indTestProducers.size(); prod++) {
                    String[] vars4 = new String[fixedIndices.length + questionMarkFirstTwoIndices.length + questionMarkRestIndices.length + choice3.length];
                    for (int i = 0; i < fixedIndices.length; i++) {
                        vars4[fixedIndices[i]] = fixedVars[i];
                    }
                    for (int i = 0; i < choice1.length; i++) {
                        vars4[questionMarkFirstTwoIndices[i]] = vars1.get(choice1[i]);
                    }
                    for (int i = 0; i < choice2.length; i++) {
                        vars4[questionMarkRestIndices[i]] = vars2.get(choice2[i]);
                    }
                    for (int i = 0; i < choice3.length; i++) {
                        vars4[plusIndices[i]] = vars3.get(choice3[i]);
                    }
                    IndependenceTest independenceTest = getIndependenceTest(prod);
                    Node x = independenceTest.getVariable(vars4[0]);
                    Node y = independenceTest.getVariable(vars4[1]);
                    List<Node> z = new ArrayList<>();
                    for (int i = 2; i < vars4.length; i++) {
                        z.add(independenceTest.getVariable(vars4[i]));
                    }
                    IndependenceResult.Type indep;
                    double pValue;
                    try {
                        indep = independenceTest.isIndependent(x, y, z) ? IndependenceResult.Type.INDEPENDENT : IndependenceResult.Type.DEPENDENT;
                        pValue = independenceTest.getPValue();
                    } catch (Exception e) {
                        indep = IndependenceResult.Type.UNDETERMINED;
                        pValue = Double.NaN;
                    }
                    results.get(results.size() - 1).add(new IndependenceResult(results.size(), factString(x, y, z), indep, pValue));
                }
                if (results.size() > getListLimit())
                    break LOOP;
            }
        }
    }
    model.setResults(results);
    tableModel.fireTableDataChanged();
}

Example 7 with IndependenceTest

use of edu.cmu.tetrad.search.IndependenceTest in project tetrad by cmu-phil.

the class MBFS 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.Mbfs search = new edu.cmu.tetrad.search.Mbfs(test, parameters.getInt("depth"));
        search.setDepth(parameters.getInt("depth"));
        search.setKnowledge(knowledge);
        this.targetName = parameters.getString("targetName");
        if (targetName.isEmpty()) {
            throw new IllegalArgumentException("Target variable name needs to be provided.");
        }
        if (test.getVariable(targetName) == null) {
            throw new IllegalArgumentException("Target variable name '" + targetName + "' not found in dataset.");
        }
        Node target = test.getVariable(targetName);
        return search.search(target.getName());
    } else {
        MBFS algorithm = new MBFS(test);
        // algorithm.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 8 with IndependenceTest

use of edu.cmu.tetrad.search.IndependenceTest in project tetrad by cmu-phil.

the class ImagesPcStableMax method search.

@Override
public Graph search(List<DataModel> dataModels, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        List<DataSet> dataSets = new ArrayList<>();
        for (DataModel dataModel : dataModels) {
            dataSets.add((DataSet) dataModel);
        }
        SemBicScoreImages3 score = new SemBicScoreImages3(dataSets);
        score.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
        IndependenceTest test = new IndTestScore(score);
        PcStableMax search = new PcStableMax(test);
        search.setUseHeuristic(parameters.getBoolean("useMaxPOrientationHeuristic"));
        search.setMaxPathLength(parameters.getInt("maxPOrientationMaxPathLength"));
        search.setKnowledge(knowledge);
        search.setDepth(parameters.getInt("depth"));
        return search.search();
    } else {
        ImagesPcStableMax imagesPcStableMax = new ImagesPcStableMax();
        // imagesPcStableMax.setKnowledge(knowledge);
        List<DataSet> datasets = new ArrayList<>();
        for (DataModel dataModel : dataModels) {
            datasets.add((DataSet) dataModel);
        }
        GeneralBootstrapTest search = new GeneralBootstrapTest(datasets, imagesPcStableMax, 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 9 with IndependenceTest

use of edu.cmu.tetrad.search.IndependenceTest in project tetrad by cmu-phil.

the class TsImages method search.

@Override
public Graph search(DataModel dataModel, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        DataSet dataSet = (DataSet) dataModel;
        TsGFci search;
        Score score1 = score.getScore(dataSet, parameters);
        IndependenceTest test = new IndTestScore(score1);
        search = new TsGFci(test, score1);
        search.setKnowledge(dataSet.getKnowledge());
        return search.search();
    } else {
        TsImages algorithm = new TsImages(score);
        DataSet data = (DataSet) dataModel;
        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 10 with IndependenceTest

use of edu.cmu.tetrad.search.IndependenceTest in project tetrad by cmu-phil.

the class TestIndTestFisherZ method testDirections.

@Test
public void testDirections() {
    RandomUtil.getInstance().setSeed(48285934L);
    Graph graph1 = new EdgeListGraph();
    Graph graph2 = new EdgeListGraph();
    Node x = new GraphNode("X");
    Node y = new GraphNode("Y");
    Node z = new GraphNode("Z");
    graph1.addNode(x);
    graph1.addNode(y);
    graph1.addNode(z);
    graph2.addNode(x);
    graph2.addNode(y);
    graph2.addNode(z);
    graph1.addEdge(Edges.directedEdge(x, y));
    graph1.addEdge(Edges.directedEdge(y, z));
    graph2.addEdge(Edges.directedEdge(x, y));
    graph2.addEdge(Edges.directedEdge(z, y));
    SemPm pm1 = new SemPm(graph1);
    SemPm pm2 = new SemPm(graph2);
    SemIm im1 = new SemIm(pm1);
    SemIm im2 = new SemIm(pm2);
    im2.setEdgeCoef(x, y, im1.getEdgeCoef(x, y));
    im2.setEdgeCoef(z, y, im1.getEdgeCoef(y, z));
    DataSet data1 = im1.simulateData(500, false);
    DataSet data2 = im2.simulateData(500, false);
    IndependenceTest test1 = new IndTestFisherZ(data1, 0.05);
    IndependenceTest test2 = new IndTestFisherZ(data2, 0.05);
    test1.isIndependent(data1.getVariable(x.getName()), data1.getVariable(y.getName()));
    double p1 = test1.getPValue();
    test2.isIndependent(data2.getVariable(x.getName()), data2.getVariable(z.getName()), data2.getVariable(y.getName()));
    double p2 = test2.getPValue();
    test2.isIndependent(data2.getVariable(x.getName()), data2.getVariable(z.getName()));
    double p3 = test2.getPValue();
    assertEquals(0, p1, 0.01);
    assertEquals(0, p2, 0.01);
    assertEquals(0.38, p3, 0.01);
}