Example usage for org.apache.commons.math.stat.descriptive.rank Median Median

Introduction

In this page you can find the example usage for org.apache.commons.math.stat.descriptive.rank Median Median.

Prototype

public Median() 

Source Link

Document

Default constructor.

Usage

From source file:cs.cirg.cida.components.SynopsisTableModel.java

@Override
public Object getValueAt(int rowIndex, int columnIndex) {
    if (columnIndex == 0) {
        return experiments.get(rowIndex).getName();
    }//from  w  ww  . j  a v  a  2  s  .  com
    if (columnIndex % 3 == 1) {
        DescriptiveStatistics descriptiveStatistics = experiments.get(rowIndex)
                .getBottomRowStatistics(variables.get((columnIndex - 1) / 3));
        return descriptiveStatistics.getMean();
    }
    if (columnIndex % 3 == 2) {
        DescriptiveStatistics descriptiveStatistics = experiments.get(rowIndex)
                .getBottomRowStatistics(variables.get((columnIndex - 1) / 3));
        return descriptiveStatistics.apply(new Median());
    }
    DescriptiveStatistics descriptiveStatistics = experiments.get(rowIndex)
            .getBottomRowStatistics(variables.get((columnIndex - 1) / 3));
    return descriptiveStatistics.getStandardDeviation();
}

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From source file:fr.ens.transcriptome.teolenn.util.MathUtils.java

/**
 * Calc the median of an array of double
 * @param data Data//from w w w .  j av a2s . c o  m
 * @param noNaN true if NaN value must be removed from the computation
 * @return the median or NaN if the data is null
 */
public static double median(final double[] data, final boolean noNaN) {

    if (data == null)
        return Double.NaN;

    Median median = new Median();
    return median.evaluate(noNaN ? removeNaN(data) : data);
}

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From source file:ch.ethz.bsse.quasirecomb.informationholder.ModelSelectionBootstrapStorage.java

public SelectionResultBootstrap(Collection<Double> bics) {
    List<Double> list = new ArrayList<>(bics);
    double[] bicsTmp = new double[list.size()];
    for (int i = 0; i < list.size(); i++) {
        bicsTmp[i] = list.get(i);// w  w w . j  a va  2  s  . co  m
    }
    this.median = new Median().evaluate(bicsTmp);
    this.lowerBound = median - new StandardDeviation().evaluate(bicsTmp) * Math.sqrt(1 + 1d / bicsTmp.length);
}

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From source file:ch.ethz.bsse.quasirecomb.model.hmm.EM.java

private void blackbox(Read[] reads, int N, int L, int K, int n) {
    Globals.getINSTANCE().setLOG(new StringBuilder());
    Globals.getINSTANCE().setMAX_LLH(-1);
    Globals.getINSTANCE().setMIN_BIC(Double.MAX_VALUE);
    String pathOptimum = null;/*w ww .jav  a  2s .c  o  m*/
    if (K == 1 || Globals.getINSTANCE().isFORCE_NO_RECOMB()) {
        Globals.getINSTANCE().setNO_RECOMB(true);
    } else {
        Globals.getINSTANCE().setNO_RECOMB(false);
    }
    if (Globals.getINSTANCE().getOPTIMUM() == null) {
        double maxLLH = Double.NEGATIVE_INFINITY;
        bics = new Double[Globals.getINSTANCE().getREPEATS()];
        double[] bics_local = new double[Globals.getINSTANCE().getREPEATS()];
        for (int i = 0; i < Globals.getINSTANCE().getREPEATS(); i++) {
            SingleEM sem = new SingleEM(N, K, L, n, reads, Globals.getINSTANCE().getDELTA_LLH(), i);
            bics_local[i] = sem.getOptimalResult().getBIC();
            bics[i] = sem.getOptimalResult().getBIC();
            this.maxBIC = Math.max(this.maxBIC, sem.getOptimalResult().getBIC());
            if (sem.getLoglikelihood() > maxLLH) {
                maxLLH = sem.getLoglikelihood();
                pathOptimum = sem.getOptimumPath();
            }
        }
        medianBIC = new Median().evaluate(bics_local);
        lowerBoundBIC = medianBIC
                - new StandardDeviation().evaluate(bics_local) * Math.sqrt(1 + 1d / bics_local.length);
    } else {
        pathOptimum = Globals.getINSTANCE().getOPTIMUM();
    }
    if (Globals.getINSTANCE().isMODELSELECTION()) {
        try {
            FileInputStream fis = new FileInputStream(pathOptimum);
            try (ObjectInputStream in = new ObjectInputStream(fis)) {
                or = (OptimalResult) in.readObject();
            }
        } catch (IOException | ClassNotFoundException ex) {
            System.err.println(ex);
        }
        StatusUpdate.getINSTANCE().printBIC(K, (int) or.getBIC());
    } else {
        try {
            FileInputStream fis = new FileInputStream(pathOptimum);
            try (ObjectInputStream in = new ObjectInputStream(fis)) {
                or = (OptimalResult) in.readObject();
            }
        } catch (IOException | ClassNotFoundException ex) {
            System.err.println(ex);
        }

        StatusUpdate.getINSTANCE().printBIC(K, (int) or.getBIC());
        System.out.print("\n");
        if (!Globals.getINSTANCE().isSUBSAMPLE()) {
            //            Globals.getINSTANCE().setREFINEMENT(true);
            if (!Globals.getINSTANCE().isANNEALING()) {
                SingleEM bestEM = new SingleEM(or, Globals.getINSTANCE().getDELTA_REFINE_LLH(), reads);
                this.or = bestEM.getOptimalResult();
            }
            StatusUpdate.getINSTANCE().printBIC(K, 100, (int) this.or.getBIC());
            if (Globals.getINSTANCE().isLOGGING()) {
                Utils.saveFile(Globals.getINSTANCE().getSAVEPATH() + "support" + File.separator + "log_K" + K,
                        Globals.getINSTANCE().getLOG().toString());
            }
        }
    }
}

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From source file:fr.ens.transcriptome.corsen.util.StatTest.java

public void testMedian() {

    Median median = new Median();

    for (int i = 0; i < 1000; i++) {

        List<DataDouble> list = generate();
        assertEquals(median.evaluate(Stats.toDouble(list)), Stats.median(list));
    }/*  www .ja va 2s .  co  m*/
}

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From source file:edu.harvard.med.screensaver.analysis.heatmaps.HeatMap.java

private void initialize(Filter<Pair<WellKey, ResultValue>> scoringFilter,
        AggregateFunction<Double> scoringFunc) {

    Collection<Double> aggregationValues = new ArrayList<Double>();
    for (WellKey wellKey : _resultValues.keySet()) {
        if (wellKey.getPlateNumber() == _plateNumber) {
            ResultValue rv = getResultValue(wellKey.getRow(), wellKey.getColumn());
            if (rv != null && !scoringFilter.exclude(new Pair<WellKey, ResultValue>(wellKey, rv))) {
                aggregationValues.add(getRawValue(wellKey.getRow(), wellKey.getColumn()));
            }//from  w  ww.  j  av  a2 s. c om
        }
    }

    scoringFunc.initializeAggregates(aggregationValues);

    _statistics = new DescriptiveStatisticsImpl();
    ResizableDoubleArray medianValues = new ResizableDoubleArray();
    for (Double rawValue : aggregationValues) {
        double scoredValue = scoringFunc.compute(rawValue);
        _statistics.addValue(scoredValue);
        medianValues.addElement(scoredValue);
    }

    _median = new Median().evaluate(medianValues.getElements());

    _scalableColorFunction.setLowerLimit(_statistics.getMin());
    _scalableColorFunction.setUpperLimit(_statistics.getMax());
}

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From source file:fr.ens.transcriptome.corsen.calc.CorsenHistoryResults.java

/**
 * Get the median of the median of Min Distances.
 * @return thee median of the median of Min Distances
 *///  w  w  w.j a v  a2  s. c o m
public double getMedianOfMedianMinDistances() {

    return new Median().evaluate(getDistances());
}

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From source file:dr.evomodel.epidemiology.casetocase.CaseToCaseTreeLikelihood.java

public static Double[] getSummaryStatistics(Double[] variable) {

    double[] primitiveVariable = new double[variable.length];
    for (int i = 0; i < variable.length; i++) {
        primitiveVariable[i] = variable[i];
    }/*from   ww  w.  j a v  a  2s  . co m*/

    Double[] out = new Double[4];
    out[0] = (new Mean()).evaluate(primitiveVariable);
    out[1] = (new Median()).evaluate(primitiveVariable);
    out[2] = (new Variance()).evaluate(primitiveVariable);
    out[3] = Math.sqrt(out[2]);
    return out;
}

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From source file:org.apache.derbyDemo.scores.proc.Functions.java

/**
 * <p>//from   w ww  .  j a va  2s .  c  om
 * Calculate the median score achieved on a Test.
 * </p>
 */
public static double getMedianTestScore(int testID) throws SQLException {
    Logger log = Logger.getLogger();
    boolean loggingEnabled = log.isLoggingEnabled();
    Median median = new Median();
    ArrayList arraylist = new ArrayList();
    Connection conn = getDefaultConnection();

    try {
        log.enableLogging(false);

        PreparedStatement ps = Utils.prepare(conn, "select tk.score\n" + "from TestTaking tk, LastTaking lt\n"
                + "where tk.takingID = lt.takingID\n" + "and tk.testID = ?\n");

        ps.setInt(1, testID);

        ResultSet rs = ps.executeQuery();

        while (rs.next()) {
            arraylist.add(new Double(rs.getDouble(1)));
        }

        Utils.close(rs);
        Utils.close(ps);
    } finally {
        log.enableLogging(loggingEnabled);
    }

    int count = arraylist.size();
    double values[] = new double[count];

    for (int i = 0; i < count; i++) {
        values[i] = ((Double) arraylist.get(i)).doubleValue();
    }

    return median.evaluate(values);
}

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