Examples with IntegerParameter beast.core.parameter.IntegerParameter used on opensource projects

Example 11 with IntegerParameter

use of beast.core.parameter.IntegerParameter in project bacter by tgvaughan.

the class SkylinePopulationFunctionTest method test1.

@Test
public void test1() throws Exception {
    SkylinePopulationFunction skyline = new SkylinePopulationFunction();
    skyline.initByName("acg", acg, "popSizes", new RealParameter("5.0 1.0 5.0 1.0"), "groupSizes", new IntegerParameter("0 0 0 0"));
    for (double t = 0.0; t < 10; t += 0.01) assertTrue(Math.abs(t - skyline.getInverseIntensity(skyline.getIntensity(t))) < 1e-14);
}

Example 12 with IntegerParameter

use of beast.core.parameter.IntegerParameter in project bacter by tgvaughan.

the class SkylinePopulationFunction method initAndValidate.

@Override
public void initAndValidate() {
    super.initAndValidate();
    acg = acgInput.get();
    popSizes = popSizesInput.get();
    groupSizes = groupSizesInput.get();
    // Initialize groupSizes to something sensible.
    if (initGroupSizesInput.get()) {
        int nChangePoints;
        if (nGridPointsInput.get() == null)
            nChangePoints = acg.getInternalNodeCount();
        else
            nChangePoints = nGridPointsInput.get();
        Integer[] values = new Integer[popSizes.getDimension()];
        int cumulant = 0;
        for (int i = 0; i < values.length; i++) {
            values[i] = nChangePoints / values.length;
            cumulant += values[i];
        }
        values[values.length - 1] += nChangePoints - cumulant;
        IntegerParameter newParam = new IntegerParameter(values);
        newParam.setBounds(1, Integer.MAX_VALUE);
        groupSizes.assignFromWithoutID(newParam);
    }
    groupBoundaries = new double[groupSizes.getDimension()];
    intensities = new double[groupSizes.getDimension()];
    dirty = true;
}

Example 13 with IntegerParameter

use of beast.core.parameter.IntegerParameter in project bacter by tgvaughan.

the class SkylinePopulationFunctionTest method test5.

@Test
public void test5() throws Exception {
    SkylinePopulationFunction skyline = new SkylinePopulationFunction();
    skyline.initByName("acg", acg, "popSizes", new RealParameter("1.0 1.0 5.0 1.0"), "groupSizes", new IntegerParameter("0"), "nGridPoints", 5, "piecewiseLinear", true);
    for (double t = 0.0; t < 10; t += 0.01) assertTrue(Math.abs(t - skyline.getInverseIntensity(skyline.getIntensity(t))) < 1e-14);
}

Example 14 with IntegerParameter

use of beast.core.parameter.IntegerParameter in project bacter by tgvaughan.

the class SkylinePopulationFunctionTest method test6.

@Test
public void test6() throws Exception {
    SkylinePopulationFunction skyline = new SkylinePopulationFunction();
    skyline.initByName("acg", acg, "popSizes", new RealParameter("1.0 1.0 5.0 1.0"), "groupSizes", new IntegerParameter("0"), "nGridPoints", 5, "piecewiseLinear", true);
    for (CFEventList.Event cfEvent : acg.getCFEvents()) {
        double t = cfEvent.getHeight();
        assertTrue(Math.abs(t - skyline.getInverseIntensity(skyline.getIntensity(t))) < 1e-14);
    }
}

Example 15 with IntegerParameter

use of beast.core.parameter.IntegerParameter in project bacter by tgvaughan.

the class PiecewisePopulationFunction method main.

/**
 * Main method for testing.
 *
 * @param args command line arguments (unused)
 */
public static void main(String[] args) throws Exception {
    String acgString = "[&15,0,1.3905355989030808,31,770,1.597708055397074] " + "[&30,931,2.4351280458424904,36,2486,3.78055549386568] " + "[&15,941,2.0439957300083322,38,2364,6.911056700367016] " + "[&36,1091,4.285505683622974,38,2589,9.867725913197855] " + "((((10:0.5385300170206817,(17:0.116794353049212," + "((3:0.039229346597297564,12:0.039229346597297564)23:0.04582913870888949," + "13:0.08505848530618705)24:0.03173586774302495)26:0.4217356639714697)28:1.8114199763246093," + "((8:0.10883006062265468,2:0.10883006062265468)25:0.556428062025291," + "(6:0.5393311342677402,11:0.5393311342677402)29:0.12592698838020555)31:1.6846918706973453)34:1.4536824928125807," + "(1:0.47184545557390367,14:0.47184545557390367)27:3.331787030583968)37:2.9704369411362554," + "(((15:2.0624287390593707,((16:0.01825347077733299,19:0.01825347077733299)21:0.7668749128372041," + "(7:0.008018731329538273,9:0.008018731329538273)20:0.7771096522849988)32:1.2773003554448337)33:0.7487092404613747," + "4:2.8111379795207454)35:0.1331794525400949,((0:0.0243537216663141," + "5:0.0243537216663141)22:0.5681537100482162,18:0.5925074317145304)30:2.35181000034631)36:3.829751995233287)38:0.0";
    ConversionGraph acg = new ConversionGraph();
    acg.initByName("siteCount", 10000, "fromString", acgString);
    PiecewisePopulationFunction skyline = new PiecewisePopulationFunction();
    skyline.initByName("acg", acg, "popSizes", new RealParameter("1.0 1.0 5.0 1.0 2.0"), "groupSizes", new IntegerParameter("0"), "piecewiseLinear", true);
    try (PrintStream ps = new PrintStream("out.txt")) {
        ps.println("t N intensity intensityInv");
        double t = 0.0;
        while (t < 10) {
            ps.format("%g %g %g %g\n", t, skyline.getPopSize(t), skyline.getIntensity(t), skyline.getInverseIntensity(skyline.getIntensity(t)));
            t += 0.001;
        }
        ps.close();
    }
}