Examples with ContinuousVariable edu.cmu.tetrad.data.ContinuousVariable used on opensource projects

Example 36 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class TestMatrixUtils method testImpiedCovar.

@Test
public void testImpiedCovar() {
    List<Node> nodes = new ArrayList<>();
    for (int i = 0; i < 10; i++) {
        nodes.add(new ContinuousVariable("X" + (i + 1)));
    }
    Graph graph = new Dag(GraphUtils.randomGraph(nodes, 0, 10, 30, 15, 15, false));
    SemPm pm = new SemPm(graph);
    SemIm im = new SemIm(pm);
    TetradMatrix err = im.getErrCovar();
    TetradMatrix coef = im.getEdgeCoef();
    TetradMatrix implied = MatrixUtils.impliedCovar(coef, err);
    assertTrue(MatrixUtils.isPositiveDefinite(implied));
    TetradMatrix corr = MatrixUtils.convertCovToCorr(new TetradMatrix(implied));
    assertTrue(MatrixUtils.isPositiveDefinite(corr));
}

Example 37 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class TabularComparison method newExecution.

private void newExecution() {
    statistics = new ArrayList<>();
    statistics.add(new AdjacencyPrecision());
    statistics.add(new AdjacencyRecall());
    statistics.add(new ArrowheadPrecision());
    statistics.add(new ArrowheadRecall());
    statistics.add(new TwoCyclePrecision());
    statistics.add(new TwoCycleRecall());
    statistics.add(new TwoCycleFalsePositive());
    // statistics.add(new ElapsedTime());
    // statistics.add(new F1Adj());
    // statistics.add(new F1Arrow());
    // statistics.add(new MathewsCorrAdj());
    // statistics.add(new MathewsCorrArrow());
    // statistics.add(new SHD());
    List<Node> variables = new ArrayList<>();
    for (Statistic statistic : statistics) {
        variables.add(new ContinuousVariable(statistic.getAbbreviation()));
    }
    dataSet = new ColtDataSet(0, variables);
    dataSet.setNumberFormat(new DecimalFormat("0.00"));
}

Example 38 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class TabularDataTable method pasteIntoColumn.

/**
 * The row and column indices are JTable indices.
 */
private void pasteIntoColumn(int row, int col, Object value) {
    int dataRow = row - getNumLeadingRows();
    int dataCol = col - getNumLeadingCols();
    Node variable = dataSet.getVariable(dataCol);
    if (variable instanceof ContinuousVariable && value instanceof Number) {
        dataSet.setObject(dataRow, dataCol, value);
        // dataSet.setDouble(dataRow, dataCol, (Double) value);
        return;
    }
    if ("".equals(value) || value == null) {
        return;
    }
    String valueTrimmed = ((String) value).trim();
    boolean quoted = false;
    if (valueTrimmed.startsWith("\"") && valueTrimmed.endsWith("\"")) {
        value = valueTrimmed.substring(1, valueTrimmed.length() - 1);
        quoted = true;
    }
    if (!(variable instanceof DiscreteVariable) && isEmpty(dataSet, dataCol) && (quoted || !isNumber((String) value))) {
        variable = swapDiscreteColumnForContinuous(col);
    }
    if (value instanceof String && ((String) value).trim().equals("*")) {
        value = ((Variable) variable).getMissingValueMarker();
    }
    dataSet.setObject(dataRow, dataCol, value);
    pcs.firePropertyChange("modelChanged", null, null);
}

Example 39 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class GraphComparisonParams method newExecution.

// ==========================PUBLIC METHODS===========================//
public final void newExecution() {
    ContinuousVariable adjCorrect = new ContinuousVariable("ADJ_COR");
    ContinuousVariable adjFn = new ContinuousVariable("ADJ_FN");
    ContinuousVariable adjFp = new ContinuousVariable("ADJ_FP");
    ContinuousVariable arrowptCorrect = new ContinuousVariable("AHD_COR");
    ContinuousVariable arrowptFn = new ContinuousVariable("AHD_FN");
    ContinuousVariable arrowptFp = new ContinuousVariable("AHD_FP");
    ContinuousVariable adjPrec = new ContinuousVariable("ADJ_PREC");
    ContinuousVariable adjRec = new ContinuousVariable("ADJ_REC");
    ContinuousVariable arrowptPrec = new ContinuousVariable("ARROWPT_PREC");
    ContinuousVariable arrowptRec = new ContinuousVariable("ARROWPT_REC");
    ContinuousVariable shd = new ContinuousVariable("SHD");
    // ContinuousVariable twoCycleCorrect = new ContinuousVariable("TC_COR");
    // ContinuousVariable twoCycleFn = new ContinuousVariable("TC_FN");
    // ContinuousVariable twoCycleFp = new ContinuousVariable("TC_FP");
    List<Node> variables = new LinkedList<>();
    variables.add(adjCorrect);
    variables.add(adjFn);
    variables.add(adjFp);
    variables.add(arrowptCorrect);
    variables.add(arrowptFn);
    variables.add(arrowptFp);
    variables.add(adjPrec);
    variables.add(adjRec);
    variables.add(arrowptPrec);
    variables.add(arrowptRec);
    variables.add(shd);
    // variables.add(twoCycleCorrect);
    // variables.add(twoCycleFn);
    // variables.add(twoCycleFp);
    dataSet = new ColtDataSet(0, variables);
    dataSet.setNumberFormat(new DecimalFormat("0"));
}

Example 40 with ContinuousVariable

use of edu.cmu.tetrad.data.ContinuousVariable in project tetrad by cmu-phil.

the class MNLRLikelihood method getDoF.

public double getDoF(int child_index, int[] parents) {
    double dof = 0;
    Node c = variables.get(child_index);
    List<ContinuousVariable> continuous_parents = new ArrayList<>();
    List<DiscreteVariable> discrete_parents = new ArrayList<>();
    for (int p : parents) {
        Node parent = variables.get(p);
        if (parent instanceof ContinuousVariable) {
            continuous_parents.add((ContinuousVariable) parent);
        } else {
            discrete_parents.add((DiscreteVariable) parent);
        }
    }
    int p = continuous_parents.size();
    List<List<Integer>> cells = adTree.getCellLeaves(discrete_parents);
    // List<List<Integer>> cells = partition(discrete_parents, 0).cells;
    int[] continuousCols = new int[p];
    for (int j = 0; j < p; j++) continuousCols[j] = nodesHash.get(continuous_parents.get(j));
    for (List<Integer> cell : cells) {
        int r = cell.size();
        if (r > 0) {
            int degree = fDegree;
            if (fDegree < 1) {
                degree = (int) Math.floor(Math.log(r));
            }
            if (c instanceof ContinuousVariable) {
                dof += degree * continuous_parents.size() + 1;
            } else {
                dof += ((degree * continuous_parents.size()) + 1) * (((DiscreteVariable) c).getNumCategories() - 1);
            }
        }
    }
    return dof;
}