Examples with Simulation edu.cmu.tetrad.algcomparison.simulation.Simulation used on opensource projects

Example 11 with Simulation

use of edu.cmu.tetrad.algcomparison.simulation.Simulation in project tetrad by cmu-phil.

the class Comparison method printStats.

private void printStats(double[][][] statTables, Statistics statistics, Mode mode, int[] newOrder, List<AlgorithmSimulationWrapper> algorithmSimulationWrappers, List<AlgorithmWrapper> algorithmWrappers, List<SimulationWrapper> simulationWrappers, double[] utilities, Parameters parameters) {
    if (mode == Mode.Average) {
        out.println("AVERAGE STATISTICS");
    } else if (mode == Mode.StandardDeviation) {
        out.println("STANDARD DEVIATIONS");
    } else if (mode == Mode.WorstCase) {
        out.println("WORST CASE");
    } else {
        throw new IllegalStateException();
    }
    int numTables = statTables.length;
    int numStats = statistics.size();
    NumberFormat nf = new DecimalFormat("0.00");
    NumberFormat smallNf = new DecimalFormat("0.00E0");
    out.println();
    for (int u = 0; u < numTables; u++) {
        if (!graphTypeUsed[u])
            continue;
        int rows = algorithmSimulationWrappers.size() + 1;
        int cols = (isShowSimulationIndices() ? 1 : 0) + (isShowAlgorithmIndices() ? 1 : 0) + numStats + (isShowUtilities() ? 1 : 0);
        TextTable table = new TextTable(rows, cols);
        table.setTabDelimited(isTabDelimitedTables());
        int initialColumn = 0;
        if (isShowSimulationIndices()) {
            table.setToken(0, initialColumn, "Sim");
            for (int t = 0; t < algorithmSimulationWrappers.size(); t++) {
                Simulation simulation = algorithmSimulationWrappers.get(newOrder[t]).getSimulationWrapper();
                table.setToken(t + 1, initialColumn, "" + (simulationWrappers.indexOf(simulation) + 1));
            }
            initialColumn++;
        }
        if (isShowAlgorithmIndices()) {
            table.setToken(0, initialColumn, "Alg");
            for (int t = 0; t < algorithmSimulationWrappers.size(); t++) {
                AlgorithmWrapper algorithm = algorithmSimulationWrappers.get(newOrder[t]).getAlgorithmWrapper();
                table.setToken(t + 1, initialColumn, "" + (algorithmWrappers.indexOf(algorithm) + 1));
            }
            initialColumn++;
        }
        for (int statIndex = 0; statIndex < numStats; statIndex++) {
            String statLabel = statistics.getStatistics().get(statIndex).getAbbreviation();
            table.setToken(0, initialColumn + statIndex, statLabel);
        }
        if (isShowUtilities()) {
            table.setToken(0, initialColumn + numStats, "U");
        }
        for (int t = 0; t < algorithmSimulationWrappers.size(); t++) {
            for (int statIndex = 0; statIndex < numStats; statIndex++) {
                Statistic statistic = statistics.getStatistics().get(statIndex);
                final AlgorithmWrapper algorithmWrapper = algorithmSimulationWrappers.get(newOrder[t]).getAlgorithmWrapper();
                final SimulationWrapper simulationWrapper = algorithmSimulationWrappers.get(newOrder[t]).getSimulationWrapper();
                Algorithm algorithm = algorithmWrapper.getAlgorithm();
                Simulation simulation = simulationWrapper.getSimulation();
                if (algorithm instanceof HasParameterValues) {
                    parameters.putAll(((HasParameterValues) algorithm).getParameterValues());
                }
                if (simulation instanceof HasParameterValues) {
                    parameters.putAll(((HasParameterValues) simulation).getParameterValues());
                }
                final String abbreviation = statistic.getAbbreviation();
                Object[] o = parameters.getValues(abbreviation);
                if (o.length == 1 && o[0] instanceof String) {
                    table.setToken(t + 1, initialColumn + statIndex, (String) o[0]);
                    continue;
                }
                double stat = statTables[u][newOrder[t]][statIndex];
                if (stat == 0.0) {
                    table.setToken(t + 1, initialColumn + statIndex, "-");
                } else if (stat == Double.POSITIVE_INFINITY) {
                    table.setToken(t + 1, initialColumn + statIndex, "Yes");
                } else if (stat == Double.NEGATIVE_INFINITY) {
                    table.setToken(t + 1, initialColumn + statIndex, "No");
                } else if (Double.isNaN(stat)) {
                    table.setToken(t + 1, initialColumn + statIndex, "*");
                } else {
                    table.setToken(t + 1, initialColumn + statIndex, Math.abs(stat) < Math.pow(10, -smallNf.getMaximumFractionDigits()) && stat != 0 ? smallNf.format(stat) : nf.format(stat));
                }
            }
            if (isShowUtilities()) {
                table.setToken(t + 1, initialColumn + numStats, nf.format(utilities[newOrder[t]]));
            }
        }
        out.println(getHeader(u));
        out.println();
        out.println(table);
    }
}

Example 12 with Simulation

use of edu.cmu.tetrad.algcomparison.simulation.Simulation in project tetrad by cmu-phil.

the class TestFges method clarkTest.

@Test
public void clarkTest() {
    RandomGraph randomGraph = new RandomForward();
    Simulation simulation = new LinearFisherModel(randomGraph);
    Parameters parameters = new Parameters();
    parameters.set("numMeasures", 100);
    parameters.set("numLatents", 0);
    parameters.set("coefLow", 0.2);
    parameters.set("coefHigh", 0.8);
    parameters.set("avgDegree", 2);
    parameters.set("maxDegree", 100);
    parameters.set("maxIndegree", 100);
    parameters.set("maxOutdegree", 100);
    parameters.set("connected", false);
    parameters.set("numRuns", 1);
    parameters.set("differentGraphs", false);
    parameters.set("sampleSize", 1000);
    parameters.set("faithfulnessAssumed", false);
    parameters.set("maxDegree", -1);
    parameters.set("verbose", false);
    parameters.set("alpha", 0.01);
    simulation.createData(parameters);
    DataSet dataSet = (DataSet) simulation.getDataModel(0);
    Graph trueGraph = simulation.getTrueGraph(0);
    // trueGraph = SearchGraphUtils.patternForDag(trueGraph);
    ScoreWrapper score = new edu.cmu.tetrad.algcomparison.score.SemBicScore();
    IndependenceWrapper test = new FisherZ();
    Algorithm fges = new edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Fges(score, false);
    Graph fgesGraph = fges.search(dataSet, parameters);
    clarkTestForAlpha(0.05, parameters, dataSet, trueGraph, fgesGraph, test);
    clarkTestForAlpha(0.01, parameters, dataSet, trueGraph, fgesGraph, test);
}