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

Example 81 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class UCRelaxedClockModel method initAndValidate.

@Override
public void initAndValidate() {
    tree = treeInput.get();
    branchCount = tree.getNodeCount() - 1;
    categories = categoryInput.get();
    usingQuantiles = (categories == null);
    if (!usingQuantiles) {
        LATTICE_SIZE_FOR_DISCRETIZED_RATES = numberOfDiscreteRates.get();
        if (LATTICE_SIZE_FOR_DISCRETIZED_RATES <= 0)
            LATTICE_SIZE_FOR_DISCRETIZED_RATES = branchCount;
        Log.info.println("  UCRelaxedClockModel: using " + LATTICE_SIZE_FOR_DISCRETIZED_RATES + " rate " + "categories to approximate rate distribution across branches.");
    } else {
        if (numberOfDiscreteRates.get() != -1) {
            throw new RuntimeException("Can't specify both numberOfDiscreteRates and rateQuantiles inputs.");
        }
        Log.info.println("  UCRelaxedClockModel: using quantiles for rate distribution across branches.");
    }
    if (usingQuantiles) {
        quantiles = quantileInput.get();
        quantiles.setDimension(branchCount);
        Double[] initialQuantiles = new Double[branchCount];
        for (int i = 0; i < branchCount; i++) {
            initialQuantiles[i] = Randomizer.nextDouble();
        }
        RealParameter other = new RealParameter(initialQuantiles);
        quantiles.assignFromWithoutID(other);
        quantiles.setLower(0.0);
        quantiles.setUpper(1.0);
    } else {
        categories.setDimension(branchCount);
        Integer[] initialCategories = new Integer[branchCount];
        for (int i = 0; i < branchCount; i++) {
            initialCategories[i] = Randomizer.nextInt(LATTICE_SIZE_FOR_DISCRETIZED_RATES);
        }
        // set initial values of rate categories
        IntegerParameter other = new IntegerParameter(initialCategories);
        categories.assignFromWithoutID(other);
        categories.setLower(0);
        categories.setUpper(LATTICE_SIZE_FOR_DISCRETIZED_RATES - 1);
    }
    distribution = rateDistInput.get();
    if (!usingQuantiles) {
        // rates are initially zero and are computed by getRawRate(int i) as needed
        rates = new double[LATTICE_SIZE_FOR_DISCRETIZED_RATES];
        storedRates = new double[LATTICE_SIZE_FOR_DISCRETIZED_RATES];
    // System.arraycopy(rates, 0, storedRates, 0, rates.length);
    }
    normalize = normalizeInput.get();
    meanRate = meanRateInput.get();
    if (meanRate == null) {
        meanRate = new RealParameter("1.0");
    }
    try {
        double mean = rateDistInput.get().getMean();
        if (Math.abs(mean - 1.0) > 1e-6) {
            Log.warning.println("WARNING: mean of distribution for relaxed clock model is not 1.0.");
        }
    } catch (RuntimeException e) {
    // ignore
    }
}

Example 82 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class SliceOperator method proposal.

/**
 * override this for proposals,
 * returns log of hastingRatio, or Double.NEGATIVE_INFINITY if proposal should not be accepted *
 */
@Override
public double proposal(Evaluator E) {
    int m = 100;
    RealParameter X = parameterInput.get();
    // Find the density at the current point
    Double gx0 = evaluate(E);
    // System.err.println("gx0 = " + gx0);
    // Get the 1st element
    Double x0 = X.getValue(0);
    // System.err.println("x0 = " + x0);
    // Determine the slice level, in log terms.
    double logy = gx0 - Randomizer.nextExponential(1);
    // Find the initial interval to sample from.
    Double[] range = find_slice_boundaries_stepping_out(E, X, logy, windowSize, m);
    Double L = range[0];
    Double R = range[1];
    // Sample from the interval, shrinking it on each rejection
    double x_new = search_interval(E, x0, X, L, R, logy);
    X.setValue(x_new);
    if (n_learning_iterations > 0) {
        n_learning_iterations--;
        totalDelta += Math.abs(x_new - x0);
        totalNumber++;
        double W_predicted = totalDelta / totalNumber * 4.0;
        if (totalNumber > 3) {
            W = 0.95 * W + 0.05 * W_predicted;
            windowSize = W;
        }
    // System.err.println("W = " + W);
    }
    return Double.POSITIVE_INFINITY;
}

Example 83 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class UpDownOperator method proposal.

/**
 * override this for proposals,
 *
 * @return log of Hastings Ratio, or Double.NEGATIVE_INFINITY if proposal
 *         should not be accepted
 */
@Override
public final double proposal() {
    final double scale = (scaleFactor + (Randomizer.nextDouble() * ((1.0 / scaleFactor) - scaleFactor)));
    int goingUp = 0, goingDown = 0;
    if (elementWiseInput.get()) {
        int size = 0;
        for (StateNode up : upInput.get()) {
            if (size == 0)
                size = up.getDimension();
            if (size > 0 && up.getDimension() != size) {
                throw new RuntimeException("elementWise=true but parameters of differing lengths!");
            }
            goingUp += 1;
        }
        for (StateNode down : downInput.get()) {
            if (size == 0)
                size = down.getDimension();
            if (size > 0 && down.getDimension() != size) {
                throw new RuntimeException("elementWise=true but parameters of differing lengths!");
            }
            goingDown += 1;
        }
        int index = Randomizer.nextInt(size);
        for (StateNode up : upInput.get()) {
            if (up instanceof RealParameter) {
                RealParameter p = (RealParameter) up;
                p.setValue(p.getValue(index) * scale);
            }
            if (outsideBounds(up)) {
                return Double.NEGATIVE_INFINITY;
            }
        }
        for (StateNode down : downInput.get()) {
            if (down instanceof RealParameter) {
                RealParameter p = (RealParameter) down;
                p.setValue(p.getValue(index) / scale);
            }
            if (outsideBounds(down)) {
                return Double.NEGATIVE_INFINITY;
            }
        }
    } else {
        try {
            for (StateNode up : upInput.get()) {
                up = up.getCurrentEditable(this);
                goingUp += up.scale(scale);
            }
            // Same below for down
            for (StateNode up : upInput.get()) {
                if (outsideBounds(up)) {
                    return Double.NEGATIVE_INFINITY;
                }
            }
            for (StateNode down : downInput.get()) {
                down = down.getCurrentEditable(this);
                goingDown += down.scale(1.0 / scale);
            }
            for (StateNode down : downInput.get()) {
                if (outsideBounds(down)) {
                    return Double.NEGATIVE_INFINITY;
                }
            }
        } catch (Exception e) {
            // scale resulted in invalid StateNode, abort proposal
            return Double.NEGATIVE_INFINITY;
        }
    }
    return (goingUp - goingDown - 2) * Math.log(scale);
}

Example 84 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class SiteModel method initAndValidate.

@Override
public void initAndValidate() {
    // useBeast1StyleGammaInput.get();
    useBeast1StyleGamma = true;
    muParameter = muParameterInput.get();
    if (muParameter == null) {
        muParameter = new RealParameter("1.0");
    }
    shapeParameter = shapeParameterInput.get();
    invarParameter = invarParameterInput.get();
    if (invarParameter == null) {
        invarParameter = new RealParameter("0.0");
        invarParameter.setBounds(Math.max(0.0, invarParameter.getLower()), Math.min(1.0, invarParameter.getUpper()));
    }
    // if (muParameter != null) {
    muParameter.setBounds(Math.max(muParameter.getLower(), 0.0), Math.min(muParameter.getUpper(), Double.POSITIVE_INFINITY));
    // }
    if (shapeParameter != null) {
        // The quantile calculator fails when the shape parameter goes much below
        // 1E-3 so we have put a hard lower bound on it. If this is not there then
        // the category rates can go to 0 and cause a -Inf likelihood (whilst this
        // is not a problem as the state will be rejected, it could mask other issues
        // and this seems the better approach.
        shapeParameter.setBounds(Math.max(shapeParameter.getLower(), 1.0E-3), Math.min(shapeParameter.getUpper(), 1.0E3));
    }
    if (/*invarParameter != null && */
    (invarParameter.getValue() < 0 || invarParameter.getValue() > 1)) {
        throw new IllegalArgumentException("proportion invariant should be between 0 and 1");
    }
    refresh();
    addCondition(muParameterInput);
    addCondition(invarParameterInput);
    addCondition(shapeParameterInput);
}

Example 85 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class Input method setStringValue.

// determineClass
/**
 * Try to parse value of string into Integer, Double or Boolean,
 * or it this types differs, just assign as string.
 *
 * @param stringValue value representation
 * @throws IllegalArgumentException when all conversions fail
 */
@SuppressWarnings({ "unchecked", "rawtypes" })
private void setStringValue(final String stringValue, final BEASTInterface beastObject) {
    // figure out the type of T and create object based on T=Integer, T=Double, T=Boolean, T=Valuable
    if (value instanceof List<?>) {
        List list = (List) value;
        list.clear();
        // remove start and end spaces
        String stringValue2 = stringValue.replaceAll("^\\s+", "");
        stringValue2 = stringValue2.replaceAll("\\s+$", "");
        // split into space-separated bits
        String[] stringValues = stringValue2.split("\\s+");
        for (int i = 0; i < stringValues.length; i++) {
            if (theClass.equals(Integer.class)) {
                list.add(new Integer(stringValues[i % stringValues.length]));
            } else if (theClass.equals(Double.class)) {
                list.add(new Double(stringValues[i % stringValues.length]));
            } else if (theClass.equals(Boolean.class)) {
                String str = stringValues[i % stringValues.length].toLowerCase();
                list.add(str.equals("1") || str.equals("true") || str.equals("yes"));
            } else if (theClass.equals(String.class)) {
                list.add(new String(stringValues[i % stringValues.length]));
            }
        }
        return;
    }
    if (theClass.equals(Integer.class)) {
        value = (T) new Integer(stringValue);
        return;
    }
    if (theClass.equals(Long.class)) {
        value = (T) new Long(stringValue);
        return;
    }
    if (theClass.equals(Double.class)) {
        value = (T) new Double(stringValue);
        return;
    }
    if (theClass.equals(Float.class)) {
        value = (T) new Float(stringValue);
        return;
    }
    if (theClass.equals(Boolean.class)) {
        // RRB why the local parsing instead of using the Boolean c'tor?
        // final String valueString2 = stringValue.toLowerCase();
        // if (valueString2.equals("yes") || valueString2.equals("true")) {
        // value = (T) Boolean.TRUE;
        // return;
        // } else if (valueString2.equals("no") || valueString2.equals("false")) {
        // value = (T) Boolean.FALSE;
        // return;
        // }
        value = (T) new Boolean(stringValue);
        return;
    }
    if (theClass.equals(Function.class)) {
        final RealParameter param = new RealParameter();
        param.initByName("value", stringValue, "upper", 0.0, "lower", 0.0, "dimension", 1);
        param.initAndValidate();
        if (value != null && value instanceof List) {
            ((List) value).add(param);
        } else {
            value = (T) param;
        }
        param.getOutputs().add(beastObject);
        return;
    }
    if (theClass.isEnum()) {
        if (possibleValues == null) {
            possibleValues = (T[]) theClass.getDeclaringClass().getEnumConstants();
        }
        for (final T t : possibleValues) {
            if (stringValue.equals(t.toString())) {
                value = t;
                return;
            }
        }
        throw new IllegalArgumentException("Input 104: value " + stringValue + " not found. Select one of " + Arrays.toString(possibleValues));
    }
    // call a string constructor of theClass
    try {
        Constructor ctor;
        Object v = stringValue;
        try {
            ctor = theClass.getDeclaredConstructor(String.class);
        } catch (NoSuchMethodException e) {
            // try integer constructor instead
            try {
                if (stringValue.startsWith("0x")) {
                    v = Integer.parseInt(stringValue.substring(2), 16);
                } else {
                    v = Integer.parseInt(stringValue);
                }
                ctor = theClass.getDeclaredConstructor(int.class);
            } catch (NumberFormatException e2) {
                // could not parse as integer, try double instead
                v = Double.parseDouble(stringValue);
                ctor = theClass.getDeclaredConstructor(double.class);
            }
        }
        ctor.setAccessible(true);
        final Object o = ctor.newInstance(v);
        if (value != null && value instanceof List) {
            ((List) value).add(o);
        } else {
            value = (T) o;
        }
        if (o instanceof BEASTInterface) {
            ((BEASTInterface) o).getOutputs().add(beastObject);
        }
    } catch (Exception e) {
        throw new IllegalArgumentException("Input 103: type mismatch, cannot initialize input '" + getName() + "' with value '" + stringValue + "'.\nExpected something of type " + getType().getName() + ". " + (e.getMessage() != null ? e.getMessage() : ""));
    }
}