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

Example 6 with IndependenceFact

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

the class RecursivePartialCorrelation method corr.

public double corr(Node x, Node y, List<Node> z) {
    if (z.isEmpty())
        return this.corr.get(nodesMap.get(x), nodesMap.get(y));
    // if (z.size() == 1) {
    // int _x = nodesMap.get(x);
    // int _y = nodesMap.get(y);
    // int _z = nodesMap.get(z.get(0));
    // 
    // double c1 = corr.get(_x, _y);
    // double c2 = corr.get(_y, _z);
    // double c3 = corr.get(_x, _z);
    // return (c1 - c2 * c3) / sqrt(1 - c2 * c2) * sqrt(1 - c3 * c3);
    // }
    IndependenceFact spec = spec(x, y, z);
    if (memory.containsKey(spec)) {
        Double corr = memory.get(spec);
        if (corr != null)
            return corr;
    }
    Node z0 = z.get(0);
    // for (Node _z0 : z) {
    // z0 = _z0;
    // List<Node> _z = new ArrayList<Node>(z);
    // _z.remove(_z0);
    // if (memory.containsKey(spec(x, y, _z))) {
    // break;
    // }
    // }
    List<Node> _z = new ArrayList<>(z);
    _z.remove(z0);
    double corr0 = corr(x, y, _z);
    double corr1 = corr(x, z0, _z);
    double corr2 = corr(z0, y, _z);
    double corr3 = (corr0 - corr1 * corr2) / sqrt(1. - corr1 * corr1) * sqrt(1. - corr2 * corr2);
    memory.put(spec, corr3);
    return corr3;
}

Example 7 with IndependenceFact

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

the class IndependenceFactsModel method loadFacts.

public static IndependenceFactsModel loadFacts(Reader reader) throws IOException {
    IndependenceFactsModel facts = new IndependenceFactsModel();
    Set<String> names = new HashSet<>();
    Map<String, Node> nodes = new HashMap<>();
    BufferedReader in = new BufferedReader(reader);
    String line;
    while ((line = in.readLine()) != null) {
        String[] tokens = line.split("[ ,;_|]+");
        if (tokens.length == 0)
            continue;
        if (tokens.length < 2)
            throw new IllegalArgumentException("Must specify at least two variables--e.g. X1 X2, for X1 _||_ X2.");
        for (String token : tokens) {
            names.add(token);
            if (!nodes.containsKey(token)) {
                nodes.put(token, new GraphNode(token));
            }
        }
        List<Node> z = new ArrayList<>();
        for (int i = 2; i < tokens.length; i++) {
            z.add(nodes.get(tokens[i]));
        }
        facts.add(new IndependenceFact(nodes.get(tokens[0]), nodes.get(tokens[1]), z));
    }
    return facts;
}

Example 8 with IndependenceFact

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

the class TestIndependenceFact method testSimpleCase.

@Test
public void testSimpleCase() {
    Node x = new GraphNode("X");
    Node y = new GraphNode("Y");
    Node w = new GraphNode("W");
    IndependenceFact fact1 = new IndependenceFact(x, y);
    IndependenceFact fact2 = new IndependenceFact(y, x);
    assertEquals(fact1, fact2);
    IndependenceFact fact3 = new IndependenceFact(x, w);
    assertNotEquals(fact1, fact3);
    List<IndependenceFact> facts = new ArrayList<>();
    facts.add(fact1);
    assertTrue(facts.contains(fact2));
}

Example 9 with IndependenceFact

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

the class IndTestDSep method isIndependent.

/**
 * Checks the indicated d-separation fact.
 *
 * @param x one node.
 * @param y a second node.
 * @param z a List of nodes (conditioning variables)
 * @return true iff x _||_ y | z
 */
public boolean isIndependent(Node x, Node y, List<Node> z) {
    if (z == null) {
        throw new NullPointerException();
    }
    for (Node node : z) {
        if (node == null) {
            throw new NullPointerException();
        }
    }
    if (!observedVars.contains(x)) {
        throw new IllegalArgumentException("Not an observed variable: " + x);
    }
    if (!observedVars.contains(y)) {
        throw new IllegalArgumentException("Not an observed variable: " + y);
    }
    for (Node _z : z) {
        if (!observedVars.contains(_z)) {
            throw new IllegalArgumentException("Not an observed variable: " + _z);
        }
    }
    boolean dSeparated = !getGraph().isDConnectedTo(x, y, z);
    if (verbose) {
        if (dSeparated) {
            double pValue = 1.0;
            TetradLogger.getInstance().log("independencies", SearchLogUtils.independenceFactMsg(x, y, z, pValue));
            System.out.println(SearchLogUtils.independenceFactMsg(x, y, z, pValue));
        } else {
            double pValue = 0.0;
            TetradLogger.getInstance().log("dependencies", SearchLogUtils.dependenceFactMsg(x, y, z, pValue));
            System.out.println(SearchLogUtils.dependenceFactMsg(x, y, z, pValue));
        }
    }
    if (dSeparated) {
        if (this.facts != null) {
            this.facts.add(new IndependenceFact(x, y, z));
        }
        pvalue = 1.0;
    } else {
        pvalue = 0.0;
    }
    return dSeparated;
}

Example 10 with IndependenceFact

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

the class IndTestChiSquare method isIndependent.

/**
 * Determines whether variable x is independent of variable y given a list of conditioning varNames z.
 *
 * @param x the one variable being compared.
 * @param y the second variable being compared.
 * @param z the list of conditioning varNames.
 * @return true iff x _||_ y | z.
 */
public boolean isIndependent(Node x, Node y, List<Node> z) {
    NumberFormat nf = NumberFormatUtil.getInstance().getNumberFormat();
    if (z == null) {
        throw new NullPointerException();
    }
    for (Node v : z) {
        if (v == null) {
            throw new NullPointerException();
        }
    }
    // For testing x, y given z1,...,zn, set up an array of length
    // n + 2 containing the indices of these variables in order.
    int[] testIndices = new int[2 + z.size()];
    testIndices[0] = variables.indexOf(x);
    testIndices[1] = variables.indexOf(y);
    for (int i = 0; i < z.size(); i++) {
        testIndices[i + 2] = variables.indexOf(z.get(i));
    }
    // the following is lame code--need a better test
    for (int i = 0; i < testIndices.length; i++) {
        if (testIndices[i] < 0) {
            throw new IllegalArgumentException("Variable " + i + " was not used in the constructor.");
        }
    }
    ChiSquareTest.Result result = chiSquareTest.calcChiSquare(testIndices);
    this.xSquare = result.getXSquare();
    this.df = result.getDf();
    this.pValue = result.getPValue();
    if (result.isIndep()) {
        StringBuilder sb = new StringBuilder();
        sb.append("INDEPENDENCE ACCEPTED: ");
        sb.append(SearchLogUtils.independenceFact(x, y, z));
        sb.append("\tp = ").append(nf.format(result.getPValue())).append("\tx^2 = ").append(nf.format(result.getXSquare())).append("\tdf = ").append(result.getDf());
        TetradLogger.getInstance().log("independencies", sb.toString());
    }
    if (facts != null) {
        this.facts.add(new IndependenceFact(x, y, z));
    }
    return result.isIndep();
}