Examples with SemEstimator edu.cmu.tetrad.sem.SemEstimator used on opensource projects

Example 11 with SemEstimator

use of edu.cmu.tetrad.sem.SemEstimator in project tetrad by cmu-phil.

the class PcGesSearchEditor method reportIfCovMatrix.

private String reportIfCovMatrix(Graph dag, ICovarianceMatrix dataSet) {
    SemPm semPm = new SemPm(dag);
    SemEstimator estimator = new SemEstimator(dataSet, semPm);
    estimator.estimate();
    SemIm semIm = estimator.getEstimatedSem();
    NumberFormat nf = NumberFormat.getInstance();
    nf.setMaximumFractionDigits(4);
    StringBuilder buf = new StringBuilder();
    buf.append("\nDegrees of Freedom = ").append(semPm.getDof()).append(" Chi-Square = ").append(nf.format(semIm.getChiSquare())).append("\nP Value = ").append(nf.format(semIm.getPValue())).append("\nBIC Score = ").append(nf.format(semIm.getBicScore()));
    buf.append("\n\nThe above chi square test assumes that the maximum " + "likelihood function over the measured variables has been " + "maximized. Under that assumption, the null hypothesis for " + "the test is that the population covariance matrix over all " + "of the measured variables is equal to the estimated covariance " + "matrix over all of the measured variables written as a function " + "of the free model parameters--that is, the unfixed parameters " + "for each directed edge (the linear coefficient for that edge), " + "each exogenous variable (the variance for the error term for " + "that variable), and each bidirected edge (the covariance for " + "the exogenous variables it connects).  The model is explained " + "in Bollen, Structural Equations with Latent Variable, 110. ");
    return buf.toString();
}

Example 12 with SemEstimator

use of edu.cmu.tetrad.sem.SemEstimator in project tetrad by cmu-phil.

the class PcGesSearchEditor method reportIfContinuous.

private String reportIfContinuous(Graph dag, DataSet dataSet) {
    SemPm semPm = new SemPm(dag);
    SemEstimator estimator = new SemEstimator(dataSet, semPm);
    estimator.estimate();
    SemIm semIm = estimator.getEstimatedSem();
    NumberFormat nf = NumberFormat.getInstance();
    nf.setMaximumFractionDigits(4);
    StringBuilder buf = new StringBuilder();
    buf.append("\nDegrees of Freedom = ").append(semPm.getDof()).append(" Chi-Square = ").append(nf.format(semIm.getChiSquare())).append("\nP Value = ").append(nf.format(semIm.getPValue())).append("\nBIC Score = ").append(nf.format(semIm.getBicScore()));
    buf.append("\n\nThe above chi square test assumes that the maximum " + "likelihood function over the measured variables has been " + "maximized. Under that assumption, the null hypothesis for " + "the test is that the population covariance matrix over all " + "of the measured variables is equal to the estimated covariance " + "matrix over all of the measured variables written as a function " + "of the free model parameters--that is, the unfixed parameters " + "for each directed edge (the linear coefficient for that edge), " + "each exogenous variable (the variance for the error term for " + "that variable), and each bidirected edge (the covariance for " + "the exogenous variables it connects).  The model is explained " + "in Bollen, Structural Equations with Latent Variable, 110. ");
    return buf.toString();
}

Example 13 with SemEstimator

use of edu.cmu.tetrad.sem.SemEstimator in project tetrad by cmu-phil.

the class SemEstimatorEditor method resetSemImEditor.

private void resetSemImEditor() {
    java.util.List<SemEstimator> semEstimators = wrapper.getMultipleResultList();
    if (semEstimators.size() == 1) {
        SemEstimator estimatedSem = semEstimators.get(0);
        SemImEditor editor = new SemImEditor(new SemImWrapper(estimatedSem.getEstimatedSem()));
        panel.removeAll();
        panel.add(editor, BorderLayout.CENTER);
        panel.revalidate();
        panel.repaint();
    } else {
        JTabbedPane tabs = new JTabbedPane();
        for (int i = 0; i < semEstimators.size(); i++) {
            SemEstimator estimatedSem = semEstimators.get(i);
            SemImEditor editor = new SemImEditor(new SemImWrapper(estimatedSem.getEstimatedSem()));
            JPanel _panel = new JPanel();
            _panel.setLayout(new BorderLayout());
            _panel.add(editor, BorderLayout.CENTER);
            tabs.addTab(estimatedSem.getDataSet().getName(), _panel);
        }
        panel.removeAll();
        panel.add(tabs);
        panel.validate();
    }
}

Example 14 with SemEstimator

use of edu.cmu.tetrad.sem.SemEstimator in project tetrad by cmu-phil.

the class SemEstimatorEditor method compileReport.

private String compileReport() {
    StringBuilder builder = new StringBuilder();
    builder.append("Datset\tFrom\tTo\tType\tValue\tSE\tT\tP");
    java.util.List<SemEstimator> estimators = wrapper.getMultipleResultList();
    for (int i = 0; i < estimators.size(); i++) {
        SemEstimator estimator = estimators.get(i);
        SemIm estSem = estimator.getEstimatedSem();
        String dataName = estimator.getDataSet().getName();
        estSem.getFreeParameters().forEach(parameter -> {
            builder.append("\n");
            builder.append(dataName).append("\t");
            builder.append(parameter.getNodeA()).append("\t");
            builder.append(parameter.getNodeB()).append("\t");
            builder.append(typeString(parameter)).append("\t");
            builder.append(asString(paramValue(estSem, parameter))).append("\t");
            /**
             * Maximum number of free parameters for which statistics will
             * be calculated. (Calculating standard errors is high
             * complexity.) Set this to zero to turn off statistics
             * calculations (which can be problematic sometimes).
             */
            int maxFreeParamsForStatistics = 200;
            builder.append(asString(estSem.getStandardError(parameter, maxFreeParamsForStatistics))).append("\t");
            builder.append(asString(estSem.getTValue(parameter, maxFreeParamsForStatistics))).append("\t");
            builder.append(asString(estSem.getPValue(parameter, maxFreeParamsForStatistics))).append("\t");
        });
        List<Node> nodes = estSem.getVariableNodes();
        for (int j = 0; j < nodes.size(); j++) {
            Node node = nodes.get(j);
            int n = estSem.getSampleSize();
            int df = n - 1;
            double mean = estSem.getMean(node);
            double stdDev = estSem.getMeanStdDev(node);
            double stdErr = stdDev / Math.sqrt(n);
            double tValue = mean / stdErr;
            double p = 2.0 * (1.0 - ProbUtils.tCdf(Math.abs(tValue), df));
            builder.append("\n");
            builder.append(dataName).append("\t");
            builder.append(nodes.get(j)).append("\t");
            builder.append(nodes.get(j)).append("\t");
            builder.append("Mean").append("\t");
            builder.append(asString(mean)).append("\t");
            builder.append(asString(stdErr)).append("\t");
            builder.append(asString(tValue)).append("\t");
            builder.append(asString(p)).append("\t");
        }
    }
    return builder.toString();
}

Example 15 with SemEstimator

use of edu.cmu.tetrad.sem.SemEstimator in project tetrad by cmu-phil.

the class Washdown method gof.

/**
 * @return the p value of the given model.
 */
private double gof(List<List<Node>> clusters) {
    clusters = removeEmpty(clusters);
    Graph graph = pureMeasurementModel(clusters);
    SemPm pm = new SemPm(graph);
    SemEstimator estimator;
    if (cov != null) {
        estimator = new SemEstimator(cov, pm);
    } else {
        estimator = new SemEstimator(dataSet, pm);
    }
    SemIm est = estimator.estimate();
    return est.getBicScore();
}