Examples with ChoiceGenerator edu.cmu.tetrad.util.ChoiceGenerator used on opensource projects

Example 36 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class IndependenceFactsAction method generateResults.

private void generateResults() {
    this.getResults().clear();
    List<String> dataVars = getDataVars();
    if (getVars().size() < 2) {
        tableModel.fireTableDataChanged();
        return;
    }
    int minQuestionMark = 0, minPlus = 0, maxPlus = 0;
    for (int i = 2; i < getVars().size(); i++) {
        String var = getVars().get(i);
        if ("?".equals(var)) {
            minPlus++;
            maxPlus++;
        } else if ("+".equals(var)) {
            maxPlus++;
        } else {
            minQuestionMark++;
            minPlus++;
            maxPlus++;
        }
    }
    int resultIndex = -1;
    Set<Set<String>> alreadySeen = new HashSet<>();
    int xIndex = dataVars.indexOf(vars.get(0));
    int yIndex = dataVars.indexOf(vars.get(1));
    if (xIndex == -1 || yIndex == -1) {
        xIndex = 0;
        yIndex = 1;
    }
    for (int _i = 0; _i < dataVars.size(); _i++) {
        for (int _j = _i + 1; _j < dataVars.size(); _j++) {
            String _x, _y;
            if (xIndex < yIndex) {
                _x = dataVars.get(_i);
                _y = dataVars.get(_j);
            } else {
                _y = dataVars.get(_i);
                _x = dataVars.get(_j);
            }
            if (!(vars.get(0).equals("?")) && !(vars.get(0).equals("+")) && !(vars.get(0).equals(_x))) {
                continue;
            }
            if (!(vars.get(1).equals("?")) && !(vars.get(1).equals("+")) && !(vars.get(1).equals(_y))) {
                continue;
            }
            Set<String> seen = new HashSet<>();
            seen.add(_x);
            seen.add(_y);
            if (alreadySeen.contains(seen))
                continue;
            alreadySeen.add(seen);
            if (!wildcard(1) && !getVars().get(1).equals(_y)) {
                continue;
            }
            List<String> unspecifiedVars = new ArrayList<>(dataVars);
            unspecifiedVars.remove(_x);
            unspecifiedVars.remove(_y);
            Node x = getIndependenceTest().getVariable(_x);
            Node y = getIndependenceTest().getVariable(_y);
            for (int j = 2; j < getVars().size(); j++) {
                if (!wildcard(j)) {
                    unspecifiedVars.remove(getVars().get(j));
                }
            }
            for (int n = minPlus; n <= maxPlus; n++) {
                ChoiceGenerator gen2 = new ChoiceGenerator(unspecifiedVars.size(), n - minQuestionMark);
                int[] choice2;
                while ((choice2 = gen2.next()) != null) {
                    List<Node> z = new ArrayList<>();
                    for (int i = 0; i < minQuestionMark; i++) {
                        String _z = getVars().get(i + 2);
                        z.add(getIndependenceTest().getVariable(_z));
                    }
                    for (int choice : choice2) {
                        String _z = unspecifiedVars.get(choice);
                        z.add(getIndependenceTest().getVariable(_z));
                    }
                    Result.Type indep;
                    double pValue;
                    try {
                        indep = getIndependenceTest().isIndependent(x, y, z) ? Result.Type.INDEPENDENT : Result.Type.DEPENDENT;
                    } catch (Exception e) {
                        indep = Result.Type.UNDETERMINED;
                    }
                    try {
                        pValue = getIndependenceTest().getPValue();
                    } catch (Exception e) {
                        pValue = Double.NaN;
                    }
                    if (usesDSeparation()) {
                        getResults().add(new Result(++resultIndex, dsepFactString(x, y, z), indep, pValue));
                    } else {
                        getResults().add(new Result(++resultIndex, independenceFactString(x, y, z), indep, pValue));
                    }
                }
            }
        }
    }
    tableModel.fireTableDataChanged();
}

Example 37 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class GraphUtils method listColliderTriples.

public static LinkedList<Triple> listColliderTriples(Graph graph) {
    LinkedList<Triple> colliders = new LinkedList<>();
    for (Node node : graph.getNodes()) {
        List<Node> adj = graph.getAdjacentNodes(node);
        if (adj.size() < 2) {
            continue;
        }
        ChoiceGenerator gen = new ChoiceGenerator(adj.size(), 2);
        int[] choice;
        while ((choice = gen.next()) != null) {
            List<Node> others = asList(choice, adj);
            if (graph.isDefCollider(others.get(0), node, others.get(1))) {
                colliders.add(new Triple(others.get(0), node, others.get(1)));
            }
        }
    }
    return colliders;
}

Example 38 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class GraphUtils method getUnderlinedTriplesFromGraph.

/**
 * @return A list of triples of the form <X, Y, Z>, where <X, Y, Z> is a
 * definite noncollider in the given graph.
 */
public static List<Triple> getUnderlinedTriplesFromGraph(Node node, Graph graph) {
    List<Triple> underlinedTriples = new ArrayList<>();
    Set<Triple> allUnderlinedTriples = graph.getUnderLines();
    List<Node> adj = graph.getAdjacentNodes(node);
    if (adj.size() < 2) {
        return new LinkedList<>();
    }
    ChoiceGenerator gen = new ChoiceGenerator(adj.size(), 2);
    int[] choice;
    while ((choice = gen.next()) != null) {
        Node x = adj.get(choice[0]);
        Node z = adj.get(choice[1]);
        if (allUnderlinedTriples.contains(new Triple(x, node, z))) {
            underlinedTriples.add(new Triple(x, node, z));
        }
    }
    return underlinedTriples;
}

Example 39 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class GraphUtils method getDottedUnderlinedTriplesFromGraph.

/**
 * @return A list of triples of the form <X, Y, Z>, where <X, Y, Z> is a
 * definite noncollider in the given graph.
 */
public static List<Triple> getDottedUnderlinedTriplesFromGraph(Node node, Graph graph) {
    List<Triple> dottedUnderlinedTriples = new ArrayList<>();
    Set<Triple> allDottedUnderlinedTriples = graph.getDottedUnderlines();
    List<Node> adj = graph.getAdjacentNodes(node);
    if (adj.size() < 2) {
        return new LinkedList<>();
    }
    ChoiceGenerator gen = new ChoiceGenerator(adj.size(), 2);
    int[] choice;
    while ((choice = gen.next()) != null) {
        Node x = adj.get(choice[0]);
        Node z = adj.get(choice[1]);
        if (allDottedUnderlinedTriples.contains(new Triple(x, node, z))) {
            dottedUnderlinedTriples.add(new Triple(x, node, z));
        }
    }
    return dottedUnderlinedTriples;
}

Example 40 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class CcdMax method sepset.

// Returns a sepset containing the nodes in 'containing' but not the nodes in 'notContaining', or
// null if there is no such sepset.
private List<Node> sepset(Graph graph, Node a, Node c, Set<Node> containing, Set<Node> notContaining) {
    List<Node> adj = graph.getAdjacentNodes(a);
    adj.addAll(graph.getAdjacentNodes(c));
    adj.remove(c);
    adj.remove(a);
    for (int d = 0; d <= Math.min((depth == -1 ? 1000 : depth), Math.max(adj.size(), adj.size())); d++) {
        if (d <= adj.size()) {
            ChoiceGenerator gen = new ChoiceGenerator(adj.size(), d);
            int[] choice;
            while ((choice = gen.next()) != null) {
                Set<Node> v2 = GraphUtils.asSet(choice, adj);
                v2.addAll(containing);
                v2.removeAll(notContaining);
                v2.remove(a);
                v2.remove(c);
                if (!isForbidden(a, c, new ArrayList<>(v2))) {
                    getIndependenceTest().isIndependent(a, c, new ArrayList<>(v2));
                    double p2 = getIndependenceTest().getScore();
                    if (p2 < 0) {
                        return new ArrayList<>(v2);
                    }
                }
            }
        }
    }
    return null;
}