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

Example 66 with ChoiceGenerator

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

the class PurifyTetradBased method listPValues.

private List<Double> listPValues(List<Integer> cluster, boolean[] eliminated, double cutoff) {
    if (cluster.size() < 4)
        return null;
    boolean countable = false;
    List<Double> pValues = new ArrayList<>();
    ChoiceGenerator gen = new ChoiceGenerator(cluster.size(), 4);
    int[] choice;
    while ((choice = gen.next()) != null) {
        int i = choice[0];
        int j = choice[1];
        int k = choice[2];
        int l = choice[3];
        int ci = cluster.get(i);
        int cj = cluster.get(j);
        int ck = cluster.get(k);
        int cl = cluster.get(l);
        if (eliminated[ci] || eliminated[cj] || eliminated[ck] || eliminated[cl]) {
            continue;
        }
        countable = true;
        double p1 = tetradTest.tetradPValue(ci, cj, ck, cl);
        double p2 = tetradTest.tetradPValue(ci, cl, cj, ck);
        double p3 = tetradTest.tetradPValue(ci, ck, cj, cl);
        if (p1 < cutoff) {
            printTetrad(ci, cj, ck, cl, p1);
            pValues.add(p1);
        }
        if (p2 < cutoff) {
            printTetrad(ci, cl, cj, ck, p2);
            pValues.add(p2);
        }
        if (p3 < cutoff) {
            printTetrad(ci, ck, cj, cl, p3);
            pValues.add(p3);
        }
    }
    return countable ? pValues : null;
}

Example 67 with ChoiceGenerator

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

the class PossibleDsepFci method getCondSet.

private List<Node> getCondSet(Node node1, Node node2, int maxPathLength) {
    final Set<Node> possibleDsepSet = getPossibleDsep(node1, node2, maxPathLength);
    List<Node> possibleDsep = new ArrayList<>(possibleDsepSet);
    boolean noEdgeRequired = getKnowledge().noEdgeRequired(node1.getName(), node2.getName());
    List<Node> possParents = possibleParents(node1, possibleDsep, getKnowledge());
    int _depth = getDepth() == -1 ? 1000 : getDepth();
    for (int d = 0; d <= Math.min(_depth, possParents.size()); d++) {
        ChoiceGenerator cg = new ChoiceGenerator(possParents.size(), d);
        int[] choice;
        while ((choice = cg.next()) != null) {
            List<Node> condSet = GraphUtils.asList(choice, possParents);
            boolean independent = test.isIndependent(node1, node2, condSet);
            if (independent && noEdgeRequired) {
                return condSet;
            }
        }
    }
    return null;
}

Example 68 with ChoiceGenerator

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

the class ProbFci method setMinSepSet.

// ///////////////////////////////////////////////////////////////////////////
// set the sepSet of x and y to the minimal such subset of the given sepSet
// and remove the edge <x, y> if background knowledge allows
// ///////////////////////////////////////////////////////////////////////////
private void setMinSepSet(List<Node> sepSet, Node x, Node y) {
    // It is assumed that BK has been considered before calling this method
    // (for example, setting independent1 and independent2 in ruleR0_RFCI)
    /*
		// background knowledge requires this edge
		if (knowledge.noEdgeRequired(x.getNode(), y.getNode()))
		{
			return;
		}
		 */
    List<Node> empty = Collections.emptyList();
    boolean indep;
    try {
        indep = independenceTest.isIndependent(x, y, empty);
    } catch (Exception e) {
        indep = false;
    }
    if (indep) {
        getSepsets().set(x, y, empty);
        return;
    }
    int sepSetSize = sepSet.size();
    for (int i = 1; i <= sepSetSize; i++) {
        ChoiceGenerator cg = new ChoiceGenerator(sepSetSize, i);
        int[] combination;
        while ((combination = cg.next()) != null) {
            List<Node> condSet = GraphUtils.asList(combination, sepSet);
            try {
                indep = independenceTest.isIndependent(x, y, condSet);
            } catch (Exception e) {
                indep = false;
            }
            if (indep) {
                getSepsets().set(x, y, condSet);
                return;
            }
        }
    }
}

Example 69 with ChoiceGenerator

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

the class ProbFci method ruleR6R7.

/**
 * Implements Zhang's rules R6 and R7, applies them over the graph once. Orient single tails. R6: If A---Bo-*C then
 * A---B--*C. R7: If A--oBo-*C and A,C nonadjacent, then A--oB--*C
 */
private void ruleR6R7() {
    List<Node> nodes = graph.getNodes();
    for (Node b : nodes) {
        List<Node> adjacents = graph.getAdjacentNodes(b);
        if (adjacents.size() < 2)
            continue;
        ChoiceGenerator cg = new ChoiceGenerator(adjacents.size(), 2);
        for (int[] choice = cg.next(); choice != null; choice = cg.next()) {
            Node a = adjacents.get(choice[0]);
            Node c = adjacents.get(choice[1]);
            if (graph.isAdjacentTo(a, c))
                continue;
            if (!(graph.getEndpoint(b, a) == Endpoint.TAIL))
                continue;
            if (!(graph.getEndpoint(c, b) == Endpoint.CIRCLE))
                continue;
            if (graph.getEndpoint(a, b) == Endpoint.TAIL) {
                // System.out.println("Single tails (tail) " + c + " *-> " + b);
                // We know A---Bo-*C: R6 applies!
                graph.setEndpoint(c, b, Endpoint.TAIL);
                logger.log("impliedOrientations", SearchLogUtils.edgeOrientedMsg("Single tails (tail)", graph.getEdge(c, b)));
                changeFlag = true;
            }
            if (graph.getEndpoint(a, b) == Endpoint.CIRCLE) {
                // if (graph.isAdjacentTo(a, c)) continue;
                logger.log("impliedOrientations", SearchLogUtils.edgeOrientedMsg("Single tails (tail)", graph.getEdge(c, b)));
                // We know A--oBo-*C and A,C nonadjacent: R7 applies!
                graph.setEndpoint(c, b, Endpoint.TAIL);
                changeFlag = true;
            }
        }
    }
}

Example 70 with ChoiceGenerator

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

the class ProbFci method ruleR0.

// ===========================PRIVATE METHODS=========================//
/**
 * Orients colliders in the graph.  (FCI Step C)
 * <p>
 * Zhang's step F3, rule R0.
 */
private void ruleR0() {
    List<Node> nodes = graph.getNodes();
    for (Node b : nodes) {
        List<Node> adjacentNodes = graph.getAdjacentNodes(b);
        if (adjacentNodes.size() < 2) {
            continue;
        }
        ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
        int[] combination;
        while ((combination = cg.next()) != null) {
            Node a = adjacentNodes.get(combination[0]);
            Node c = adjacentNodes.get(combination[1]);
            // Skip triples that are shielded.
            if (graph.isAdjacentTo(a, c)) {
                continue;
            }
            List<Node> sepset2 = this.sepsets.get(a, c);
            if (sepset2 == null)
                continue;
            if (!sepset2.contains(b)) {
                if (!isArrowpointAllowed(a, b)) {
                    continue;
                }
                if (!isArrowpointAllowed(c, b)) {
                    continue;
                }
                graph.setEndpoint(a, b, Endpoint.ARROW);
                graph.setEndpoint(c, b, Endpoint.ARROW);
                logger.log("colliderOrientations", SearchLogUtils.colliderOrientedMsg(a, b, c));
            }
        }
    }
}