Examples with FrequencyDistribution dr.util.FrequencyDistribution used on opensource projects

Example 6 with FrequencyDistribution

use of dr.util.FrequencyDistribution in project beast-mcmc by beast-dev.

the class DensityEstimate method calculateFrequencies.

protected FrequencyDistribution calculateFrequencies(Variate data, int minimumBinCount) {
    double min = (Double) data.getMin();
    double max = (Double) data.getMax();
    if (min == max) {
        if (min == 0) {
            min = -1.0;
        } else {
            min -= Math.abs(min / 10.0);
        }
        if (max == 0) {
            max = 1.0;
        } else {
            max += Math.abs(max / 10.0);
        }
    }
    Axis axis = new LinearAxis(Axis.AT_MAJOR_TICK, Axis.AT_MAJOR_TICK);
    axis.setRange(min, max);
    int majorTickCount = axis.getMajorTickCount();
    axis.setPrefNumTicks(majorTickCount, 4);
    double binSize = axis.getMinorTickSpacing();
    int binCount = (int) ((axis.getMaxAxis() - axis.getMinAxis()) / binSize) + 2;
    if (minimumBinCount > 0) {
        while (binCount < minimumBinCount) {
            majorTickCount++;
            axis.setPrefNumTicks(majorTickCount, 4);
            binSize = axis.getMinorTickSpacing();
            // should +2, otherwise the last bar will lose
            binCount = (int) ((axis.getMaxAxis() - axis.getMinAxis()) / binSize) + 2;
        }
    }
    FrequencyDistribution frequency = new FrequencyDistribution(axis.getMinAxis(), binCount, binSize);
    for (int i = 0; i < data.getCount(); i++) {
        frequency.addValue((Double) data.get(i));
    }
    return frequency;
}

Example 7 with FrequencyDistribution

use of dr.util.FrequencyDistribution in project beast-mcmc by beast-dev.

the class KernelDensityEstimate method calculateDensity.

protected void calculateDensity(Variate data, int minimumBinCount) {
    FrequencyDistribution frequency = calculateFrequencies(data, minimumBinCount);
    xCoordinates = new Variate.D();
    yCoordinates = new Variate.D();
    double x = frequency.getLowerBound() - (frequency.getBinSize() / 2.0);
    int extraEdgeCount = 0;
    while (kde.pdf(x) > minDensity && x > lowerBoundary) {
        x -= frequency.getBinSize();
        extraEdgeCount += 1;
    }
    xCoordinates.add(x);
    yCoordinates.add(0.0);
    x += frequency.getBinSize();
    int count = 0;
    while (count < (frequency.getBinCount() + extraEdgeCount)) {
        // ||
        //                (kde.pdf(x) > minDensity && x < upperBoundary)) {
        xCoordinates.add(x);
        yCoordinates.add(kde.pdf(x));
        x += frequency.getBinSize();
        count++;
    }
    //        System.err.println("kde = " + kde.pdf(x));
    while (kde.pdf(x) > minDensity) {
        //            System.err.println("add bit on end!!!");
        xCoordinates.add(x);
        yCoordinates.add(kde.pdf(x));
        x += frequency.getBinSize();
    }
    xCoordinates.add(x);
    yCoordinates.add(0.0);
//
//
//        int extraBinsOnEdges = 5;
//        double x = frequency.getLowerBound() - extraBinsOnEdges * frequency.getBinSize();
//        for (int i = 0; i < frequency.getBinCount() + 2 * extraBinsOnEdges; i++) {
//            double xMidPoint = x + (frequency.getBinSize() / 2.0);
//            xData.add(xMidPoint);
//            yData.add(kde.pdf(xMidPoint));
//            x += frequency.getBinSize();
//        }
}