Examples with EdgeListGraph edu.cmu.tetrad.graph.EdgeListGraph used on opensource projects

Example 6 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class Mmhc method search.

/**
 * Runs PC starting with a fully connected graph over all of the variables in the domain of the independence test.
 */
public Graph search() {
    List<Node> variables = independenceTest.getVariables();
    Mmmb mmmb = new Mmmb(independenceTest, getDepth(), true);
    Map<Node, List<Node>> pc = new HashMap<>();
    for (Node x : variables) {
        pc.put(x, mmmb.getPc(x));
    }
    Graph graph = new EdgeListGraph();
    for (Node x : variables) {
        graph.addNode(x);
    }
    for (Node x : variables) {
        for (Node y : pc.get(x)) {
            if (!graph.isAdjacentTo(x, y)) {
                graph.addUndirectedEdge(x, y);
            }
        }
    }
    FgesOrienter orienter = new FgesOrienter(data);
    orienter.orient(graph);
    return graph;
}

Example 7 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class LingDisplay method resetDisplay.

private void resetDisplay() {
    String option = (String) subsetCombo.getSelectedItem();
    if ("Show All".equals(option)) {
        final List<Integer> _subsetIndices = getAllIndices(getStoredGraphs());
        subsetIndices.clear();
        subsetIndices.addAll(_subsetIndices);
        int min = subsetIndices.size() == 0 ? 0 : 1;
        final SpinnerNumberModel model = new SpinnerNumberModel(min, min, subsetIndices.size(), 1);
        model.addChangeListener(new ChangeListener() {

            public void stateChanged(ChangeEvent e) {
                int index = model.getNumber().intValue();
                workbench.setGraph(storedGraphs.getGraph(subsetIndices.get(index - 1)));
            }
        });
        spinner.setModel(model);
        totalLabel.setText(" of " + _subsetIndices.size());
        if (subsetIndices.isEmpty()) {
            workbench.setGraph(new EdgeListGraph());
        } else {
            workbench.setGraph(storedGraphs.getGraph(subsetIndices.get(0)));
        }
    } else if ("Show Stable".equals(option)) {
        final List<Integer> _subsetIndices = getStableIndices(getStoredGraphs());
        subsetIndices.clear();
        subsetIndices.addAll(_subsetIndices);
        int min = subsetIndices.size() == 0 ? 0 : 1;
        final SpinnerNumberModel model = new SpinnerNumberModel(min, min, subsetIndices.size(), 1);
        model.addChangeListener(new ChangeListener() {

            public void stateChanged(ChangeEvent e) {
                int index = model.getNumber().intValue();
                workbench.setGraph(storedGraphs.getGraph(subsetIndices.get(index - 1)));
            }
        });
        spinner.setModel(model);
        totalLabel.setText(" of " + _subsetIndices.size());
        if (subsetIndices.isEmpty()) {
            workbench.setGraph(new EdgeListGraph());
        } else {
            workbench.setGraph(storedGraphs.getGraph(subsetIndices.get(0)));
        }
    } else if ("Show Unstable".equals(option)) {
        final List<Integer> _subsetIndices = getUnstableIndices(getStoredGraphs());
        subsetIndices.clear();
        subsetIndices.addAll(_subsetIndices);
        int min = subsetIndices.size() == 0 ? 0 : 1;
        final SpinnerNumberModel model = new SpinnerNumberModel(min, min, subsetIndices.size(), 1);
        model.addChangeListener(new ChangeListener() {

            public void stateChanged(ChangeEvent e) {
                int index = model.getNumber().intValue();
                workbench.setGraph(storedGraphs.getGraph(subsetIndices.get(index - 1)));
            }
        });
        spinner.setModel(model);
        totalLabel.setText(" of " + _subsetIndices.size());
        if (subsetIndices.isEmpty()) {
            workbench.setGraph(new EdgeListGraph());
        } else {
            workbench.setGraph(storedGraphs.getGraph(subsetIndices.get(0)));
        }
    }
}

Example 8 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class IonDisplay method resetDisplay.

private void resetDisplay() {
    final List<Integer> _subsetIndices = getAllIndices(getStoredGraphs());
    indices.clear();
    indices.addAll(_subsetIndices);
    int min = indices.size() == 0 ? 0 : 1;
    final SpinnerNumberModel model = new SpinnerNumberModel(min, min, indices.size(), 1);
    model.addChangeListener(new ChangeListener() {

        public void stateChanged(ChangeEvent e) {
            int index = model.getNumber().intValue();
            workbench.setGraph(storedGraphs.get(indices.get(index - 1)));
        }
    });
    spinner.setModel(model);
    totalLabel.setText(" of " + _subsetIndices.size());
    if (indices.isEmpty()) {
        workbench.setGraph(new EdgeListGraph());
    } else {
        workbench.setGraph(storedGraphs.get(indices.get(0)));
    }
}

Example 9 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class Comparison method compare.

/**
 * Simulates data from model paramerizing the given DAG, and runs the algorithm on that data,
 * printing out error statistics.
 */
public static ComparisonResult compare(ComparisonParameters params) {
    DataSet dataSet;
    Graph trueDag;
    IndependenceTest test = null;
    Score score = null;
    ComparisonResult result = new ComparisonResult(params);
    if (params.getDataFile() != null) {
        dataSet = loadDataFile(params.getDataFile());
        if (params.getGraphFile() == null) {
            throw new IllegalArgumentException("True graph file not set.");
        }
        trueDag = loadGraphFile(params.getGraphFile());
    } else {
        if (params.getNumVars() == -1) {
            throw new IllegalArgumentException("Number of variables not set.");
        }
        if (params.getNumEdges() == -1) {
            throw new IllegalArgumentException("Number of edges not set.");
        }
        if (params.getDataType() == ComparisonParameters.DataType.Continuous) {
            List<Node> nodes = new ArrayList<>();
            for (int i = 0; i < params.getNumVars(); i++) {
                nodes.add(new ContinuousVariable("X" + (i + 1)));
            }
            trueDag = GraphUtils.randomGraphRandomForwardEdges(nodes, 0, params.getNumEdges(), 10, 10, 10, false, true);
            if (params.getDataType() == null) {
                throw new IllegalArgumentException("Data type not set or inferred.");
            }
            if (params.getSampleSize() == -1) {
                throw new IllegalArgumentException("Sample size not set.");
            }
            LargeScaleSimulation sim = new LargeScaleSimulation(trueDag);
            dataSet = sim.simulateDataFisher(params.getSampleSize());
        } else if (params.getDataType() == ComparisonParameters.DataType.Discrete) {
            List<Node> nodes = new ArrayList<>();
            for (int i = 0; i < params.getNumVars(); i++) {
                nodes.add(new DiscreteVariable("X" + (i + 1), 3));
            }
            trueDag = GraphUtils.randomGraphRandomForwardEdges(nodes, 0, params.getNumEdges(), 10, 10, 10, false, true);
            if (params.getDataType() == null) {
                throw new IllegalArgumentException("Data type not set or inferred.");
            }
            if (params.getSampleSize() == -1) {
                throw new IllegalArgumentException("Sample size not set.");
            }
            int[] tiers = new int[nodes.size()];
            for (int i = 0; i < nodes.size(); i++) {
                tiers[i] = i;
            }
            BayesPm pm = new BayesPm(trueDag, 3, 3);
            MlBayesIm im = new MlBayesIm(pm, MlBayesIm.RANDOM);
            dataSet = im.simulateData(params.getSampleSize(), false, tiers);
        } else {
            throw new IllegalArgumentException("Unrecognized data type.");
        }
        if (dataSet == null) {
            throw new IllegalArgumentException("No data set.");
        }
    }
    if (params.getIndependenceTest() == ComparisonParameters.IndependenceTestType.FisherZ) {
        if (params.getDataType() != null && params.getDataType() != ComparisonParameters.DataType.Continuous) {
            throw new IllegalArgumentException("Data type previously set to something other than continuous.");
        }
        if (Double.isNaN(params.getAlpha())) {
            throw new IllegalArgumentException("Alpha not set.");
        }
        test = new IndTestFisherZ(dataSet, params.getAlpha());
        params.setDataType(ComparisonParameters.DataType.Continuous);
    } else if (params.getIndependenceTest() == ComparisonParameters.IndependenceTestType.ChiSquare) {
        if (params.getDataType() != null && params.getDataType() != ComparisonParameters.DataType.Discrete) {
            throw new IllegalArgumentException("Data type previously set to something other than discrete.");
        }
        if (Double.isNaN(params.getAlpha())) {
            throw new IllegalArgumentException("Alpha not set.");
        }
        test = new IndTestChiSquare(dataSet, params.getAlpha());
        params.setDataType(ComparisonParameters.DataType.Discrete);
    }
    if (params.getScore() == ScoreType.SemBic) {
        if (params.getDataType() != null && params.getDataType() != ComparisonParameters.DataType.Continuous) {
            throw new IllegalArgumentException("Data type previously set to something other than continuous.");
        }
        if (Double.isNaN(params.getPenaltyDiscount())) {
            throw new IllegalArgumentException("Penalty discount not set.");
        }
        SemBicScore semBicScore = new SemBicScore(new CovarianceMatrixOnTheFly(dataSet));
        semBicScore.setPenaltyDiscount(params.getPenaltyDiscount());
        score = semBicScore;
        params.setDataType(ComparisonParameters.DataType.Continuous);
    } else if (params.getScore() == ScoreType.BDeu) {
        if (params.getDataType() != null && params.getDataType() != ComparisonParameters.DataType.Discrete) {
            throw new IllegalArgumentException("Data type previously set to something other than discrete.");
        }
        if (Double.isNaN(params.getSamplePrior())) {
            throw new IllegalArgumentException("Sample prior not set.");
        }
        if (Double.isNaN(params.getStructurePrior())) {
            throw new IllegalArgumentException("Structure prior not set.");
        }
        score = new BDeuScore(dataSet);
        ((BDeuScore) score).setSamplePrior(params.getSamplePrior());
        ((BDeuScore) score).setStructurePrior(params.getStructurePrior());
        params.setDataType(ComparisonParameters.DataType.Discrete);
        params.setDataType(ComparisonParameters.DataType.Discrete);
    }
    if (params.getAlgorithm() == null) {
        throw new IllegalArgumentException("Algorithm not set.");
    }
    long time1 = System.currentTimeMillis();
    if (params.getAlgorithm() == ComparisonParameters.Algorithm.PC) {
        if (test == null)
            throw new IllegalArgumentException("Test not set.");
        Pc search = new Pc(test);
        result.setResultGraph(search.search());
        result.setCorrectResult(SearchGraphUtils.patternForDag(new EdgeListGraph(trueDag)));
    } else if (params.getAlgorithm() == ComparisonParameters.Algorithm.CPC) {
        if (test == null)
            throw new IllegalArgumentException("Test not set.");
        Cpc search = new Cpc(test);
        result.setResultGraph(search.search());
        result.setCorrectResult(SearchGraphUtils.patternForDag(new EdgeListGraph(trueDag)));
    } else if (params.getAlgorithm() == ComparisonParameters.Algorithm.PCLocal) {
        if (test == null)
            throw new IllegalArgumentException("Test not set.");
        PcLocal search = new PcLocal(test);
        result.setResultGraph(search.search());
        result.setCorrectResult(SearchGraphUtils.patternForDag(new EdgeListGraph(trueDag)));
    } else if (params.getAlgorithm() == ComparisonParameters.Algorithm.PCStableMax) {
        if (test == null)
            throw new IllegalArgumentException("Test not set.");
        PcStableMax search = new PcStableMax(test);
        result.setResultGraph(search.search());
        result.setCorrectResult(SearchGraphUtils.patternForDag(new EdgeListGraph(trueDag)));
    } else if (params.getAlgorithm() == ComparisonParameters.Algorithm.FGES) {
        if (score == null)
            throw new IllegalArgumentException("Score not set.");
        Fges search = new Fges(score);
        search.setFaithfulnessAssumed(params.isOneEdgeFaithfulnessAssumed());
        result.setResultGraph(search.search());
        result.setCorrectResult(SearchGraphUtils.patternForDag(new EdgeListGraph(trueDag)));
    } else if (params.getAlgorithm() == ComparisonParameters.Algorithm.FGES2) {
        if (score == null)
            throw new IllegalArgumentException("Score not set.");
        Fges search = new Fges(score);
        search.setFaithfulnessAssumed(params.isOneEdgeFaithfulnessAssumed());
        result.setResultGraph(search.search());
        result.setCorrectResult(SearchGraphUtils.patternForDag(new EdgeListGraph(trueDag)));
    } else if (params.getAlgorithm() == ComparisonParameters.Algorithm.FCI) {
        if (test == null)
            throw new IllegalArgumentException("Test not set.");
        Fci search = new Fci(test);
        result.setResultGraph(search.search());
        result.setCorrectResult(new DagToPag(trueDag).convert());
    } else if (params.getAlgorithm() == ComparisonParameters.Algorithm.GFCI) {
        if (test == null)
            throw new IllegalArgumentException("Test not set.");
        GFci search = new GFci(test, score);
        result.setResultGraph(search.search());
        result.setCorrectResult(new DagToPag(trueDag).convert());
    } else {
        throw new IllegalArgumentException("Unrecognized algorithm.");
    }
    long time2 = System.currentTimeMillis();
    long elapsed = time2 - time1;
    result.setElapsed(elapsed);
    result.setTrueDag(trueDag);
    return result;
}

Example 10 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class TestSemVarMeans method constructGraph1.

private Graph constructGraph1() {
    Graph graph = new EdgeListGraph();
    Node x1 = new GraphNode("X1");
    Node x2 = new GraphNode("X2");
    Node x3 = new GraphNode("X3");
    Node x4 = new GraphNode("X4");
    Node x5 = new GraphNode("X5");
    // x1.setNodeType(NodeType.LATENT);
    // x2.setNodeType(NodeType.LATENT);
    graph.addNode(x1);
    graph.addNode(x2);
    graph.addNode(x3);
    graph.addNode(x4);
    graph.addNode(x5);
    graph.addDirectedEdge(x1, x2);
    graph.addDirectedEdge(x2, x3);
    graph.addDirectedEdge(x3, x4);
    graph.addDirectedEdge(x1, x4);
    graph.addDirectedEdge(x4, x5);
    return graph;
}