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Java RealParameter.getValue方法代码示例

本文整理汇总了Java中beast.core.parameter.RealParameter.getValue方法的典型用法代码示例。如果您正苦于以下问题：Java RealParameter.getValue方法的具体用法？Java RealParameter.getValue怎么用？Java RealParameter.getValue使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类beast.core.parameter.RealParameter的用法示例。


在下文中一共展示了RealParameter.getValue方法的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。

示例1: branchLogP

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
@Override
public double branchLogP(int speciesTreeNodeNumber, Node speciesTreeNode, double ploidy, double[] branchCoalescentTimes, int branchLineageCount, int branchEventCount) {
    final RealParameter tipPopSizes = tipPopSizesInput.get();
    final RealParameter topPopSizes = topPopSizesInput.get();

    double branchTipPopSize;
    if (speciesTreeNode.isLeaf()) {
        branchTipPopSize = tipPopSizes.getValue(speciesTreeNodeNumber);
    } else {
        final int leftChildTopI = speciesTreeNode.getLeft().getNr();
        final int rightChildTopI = speciesTreeNode.getRight().getNr();
        branchTipPopSize = topPopSizes.getValue(leftChildTopI) + topPopSizes.getValue(rightChildTopI);
    }

    if (speciesTreeNode.isRoot()) {
        return ConstantPopulations.constantLogP(branchTipPopSize, ploidy, branchCoalescentTimes, branchLineageCount, branchEventCount);
    } else {
        final int speciesTopI = speciesTreeNodeNumber;
        final double branchTopPopSize = topPopSizes.getValue(speciesTopI);
        return linearLogP(branchTopPopSize, branchTipPopSize, ploidy, branchCoalescentTimes, branchLineageCount, branchEventCount);
    }
}
开发者ID:genomescale，项目名称:starbeast2，代码行数:23，代码来源:LinearWithConstantRoot.java

示例2: serialize

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
@Override
public void serialize(Node speciesTreeNode, StringBuffer buf, DecimalFormat df) {
    final RealParameter tipPopSizes = tipPopSizesInput.get();
    final RealParameter topPopSizes = topPopSizesInput.get();
    final int speciesTreeNodeNumber = speciesTreeNode.getNr();

    double branchTipPopSize;
    if (speciesTreeNode.isLeaf()) {
        branchTipPopSize = tipPopSizes.getValue(speciesTreeNodeNumber);
    } else {
        final int leftChildTopI = speciesTreeNode.getLeft().getNr();
        final int rightChildTopI = speciesTreeNode.getRight().getNr();
        branchTipPopSize = topPopSizes.getValue(leftChildTopI) + topPopSizes.getValue(rightChildTopI);
    }

    final double branchTopPopSize = (speciesTreeNode.isRoot()) ? branchTipPopSize : topPopSizes.getValue(speciesTreeNode.getNr());

    if (df == null) buf.append("dmv={" + branchTopPopSize + "," + branchTipPopSize + "}");
    else buf.append("dmv={" + df.format(branchTopPopSize) + "," + df.format(branchTipPopSize) + "}");
}
开发者ID:genomescale，项目名称:starbeast2，代码行数:21，代码来源:LinearWithConstantRoot.java

示例3: update

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
private void update() {
    final Boolean[] indicators = indicatorsInput.get().getValues();
    final Double[] rates = branchRatesInput.get().getValues();
    final Node treeRoot = treeInput.get().getRoot();
    final double treeHeight = treeRoot.getHeight();

    double estimatedMean;
    final RealParameter estimatedMeanParameter = meanRateInput.get();
    if (estimatedMeanParameter == null) {
        estimatedMean = 1.0;
    } else {
        estimatedMean = estimatedMeanParameter.getValue();
    }

    ratesArray[rootNodeNumber] = estimatedMean;

    strictRatesTotal = 0.0;
    relaxedRatesTotal = 0.0;
    recurseBranchRates(treeRoot, treeHeight, 1.0, indicators, rates);

    // normalize the weighted average of branch rates to equal the mean rate parameter
    double scaleFactor = estimatedMean * strictRatesTotal / relaxedRatesTotal;
    for (int i = 0; i < rootNodeNumber; i++) {
        ratesArray[i] = ratesArray[i] * scaleFactor; 
    }
}
开发者ID:genomescale，项目名称:starbeast2，代码行数:27，代码来源:RandomLocalRates.java

示例4: calculateUnscaledBranchRates

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
/**
 * This is a recursive function that does the work of
 * calculating the unscaled branch rates across the tree
 * taking into account the indicator variables.
 *
 * @param node the node
 * @param rate the rate of the parent node
 */
private void calculateUnscaledBranchRates(Node node, double rate, BooleanParameter indicators, RealParameter rates) {

    int nodeNumber = getNr(node);

    if (!node.isRoot()) {
        if (indicators.getValue(nodeNumber)) {
            if (ratesAreMultipliers) {
                rate *= rates.getValue(nodeNumber);
            } else {
                rate = rates.getValue(nodeNumber);
            }
        }
    }
    unscaledBranchRates[nodeNumber] = rate;

    if (!node.isLeaf()) {
        calculateUnscaledBranchRates(node.getLeft(), rate, indicators, rates);
        calculateUnscaledBranchRates(node.getRight(), rate, indicators, rates);
    }
}
开发者ID:CompEvol，项目名称:beast2，代码行数:29，代码来源:RandomLocalClockModel.java

示例5: initAndValidate

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
public void initAndValidate(){
    df = dfInput.get();
    RealParameter scaleMatrix1d = scaleMatrixInput.get();
    dim = (int)Math.sqrt(scaleMatrix1d.getDimension());
    scaleMatrix = new double[dim][dim];
    int k = 0;
    for(int i = 0; i < dim;i++){
        for(int j = 0; j < dim; j++){
            scaleMatrix[i][j] =  scaleMatrix1d.getValue(k++);
            //System.out.print(scaleMatrix[i][j]+" ");
        }
        //System.out.println();
    }
    refresh();

}
开发者ID:jessiewu，项目名称:substBMA，代码行数:17，代码来源:Wishart.java

示例6: proposal

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
/**
 * override this for proposals,
 * returns log of hastingRatio, or Double.NEGATIVE_INFINITY if proposal should not be accepted *
 */
@Override
public double proposal() {
    RealParameter param = parameterInput.get(this);
    int i = Randomizer.nextInt(param.getDimension());
    double value = param.getValue(i);
    double newValue = getProposedVal(
            value, //original value
            i,     //index of the value
            useGaussian, //whether to use gaussian moves
            windowSizes);   //window sizes

    if (newValue < param.getLower() || newValue > param.getUpper()) {
    	return Double.NEGATIVE_INFINITY;
    }
    if (newValue == value) {
    	// this saves calculating the posterior
    	return Double.NEGATIVE_INFINITY;
    }

    param.setValue(i, newValue);
    lastChangedValueIndex = i;


    return 0.0;
}
开发者ID:jessiewu，项目名称:substBMA，代码行数:30，代码来源:ExtendedRealRandomWalkOperator.java

示例7: proposal

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
public double proposal() {

        RealParameter param = parameterInput.get(this);


        double value = param.getValue(index);
        double newValue = value;
        if (useGaussian) {
            newValue += Randomizer.nextGaussian() * windowSize;
        } else {
            newValue += Randomizer.nextDouble() * 2 * windowSize - windowSize;
        }

        if (newValue < param.getLower() || newValue > param.getUpper()) {
            return Double.NEGATIVE_INFINITY;
        }
        if (newValue == value) {
            // this saves calculating the posterior
            return Double.NEGATIVE_INFINITY;
        }

        param.setValue(index, newValue);

        return 0.0;
    }
开发者ID:jessiewu，项目名称:substBMA，代码行数:26，代码来源:SpecificRealRandomWalkOperator.java

示例8: initAndValidate

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
public void initAndValidate(){
    df = dfInput.get();
    RealParameter scaleMatrixParam = scaleMatrixInput.get();
    dim = (int)(Math.sqrt(scaleMatrixParam.getDimension()));
    scaleMatrixInv = new double[dim][dim];
    int k = 0;
    for(int i = 0; i < dim; i++){
        for(int j = 0; j < dim; j++){
            scaleMatrixInv[i][j] = scaleMatrixParam.getValue(k++);

        }

    }

    scaleMatrixInv = (new Matrix(scaleMatrixInv)).inverse().toComponents();
    mean = meanInput.get();
    x = xInput.get();

}
开发者ID:jessiewu，项目名称:substBMA，代码行数:20，代码来源:PrecisionWishartSampler.java

示例9: proposal

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
@Override
public double proposal() {

    Tree tree = treeInput.get();
    final RealParameter rParameter = rInput.get(this);

    double r = rParameter.getValue();

    if (r != 1 && ((ZeroBranchSATree)tree).getDirectAncestorNodeCount() == 0) {
        rParameter.setValue(1.);
        return 0.0;
    } else if (r == 1) {
        rParameter.setValue(Randomizer.nextDouble());
        return 0.0;
    } else return Double.NEGATIVE_INFINITY;


}
开发者ID:CompEvol，项目名称:sampled-ancestors，代码行数:19，代码来源:JumpToPoint.java

示例10: proposal

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
/**
 * override this for proposals,
 * returns log of hastingRatio, or Double.NEGATIVE_INFINITY if proposal should not be accepted *
 */
@Override
public double proposal() {

    RealParameter param = parameterInput.get(this);
    for (int i = 0; i < param.getDimension(); i++){
     double value = param.getValue(i);
     double newValue = value;
     double windowSize = 0.0;
     
    	if (indicatorInput.get().getArrayValue(i) > 0.5)
    		windowSize = windowSizeOn;
    	else
    		windowSize = windowSizeOff;
    		

     if (useGaussian) {
         newValue += Randomizer.nextGaussian() * windowSize;
     } else {
         newValue += Randomizer.nextDouble() * 2 * windowSize - windowSize;
     }
	
     if (newValue < param.getLower() || newValue > param.getUpper()) {
         return Double.NEGATIVE_INFINITY;
     }
     if (newValue == value) {
         // this saves calculating the posterior
         return Double.NEGATIVE_INFINITY;
     }
	
     param.setValue(i, newValue);
    }
    return 0.0;
}
开发者ID:nicfel，项目名称:Mascot，代码行数:38，代码来源:RealRandomWalkOperator.java

示例11: update

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
private void update() {
    if (useLogNormal && (binRatesNeedsUpdate || noCache)) {
        // set the mean in real space to equal 1
        currentLogNormalStdev = stdevInput.get().getValue();
        final double newMean = -(0.5 * currentLogNormalStdev * currentLogNormalStdev);
        final NormalDistribution normalDistr = new NormalDistributionImpl(newMean, currentLogNormalStdev);

        try {
            for (int i = 0; i < nBins; i++) {
                binRates[i] = Math.exp(normalDistr.inverseCumulativeProbability((i + 0.5) / nBins));
            }
        } catch (MathException e) {
            throw new RuntimeException("Failed to compute inverse cumulative probability!");
        }
    }

    Double estimatedMean;
    final RealParameter estimatedMeanParameter = meanRateInput.get();
    if (estimatedMeanParameter == null) {
        estimatedMean = 1.0;
    } else {
        estimatedMean = estimatedMeanParameter.getValue();
    }

    final Integer[] branchRatePointers = branchRatesInput.get().getValues();
    for (int i = 0; i < nEstimatedRates; i++) {
        int b = branchRatePointers[i];
        ratesArray[i] = binRates[b] * estimatedMean;
    }

    if (!estimateRoot) ratesArray[rootNodeNumber] = estimatedMean;

    /* StringBuffer x = new StringBuffer();
    x.append(treeInput.get().getID());
    for (int i = 0; i < ratesArray.length; i++) {
        x.append(" ");
        x.append(ratesArray[i]);
    }
    System.out.println(x); */
}
开发者ID:genomescale，项目名称:starbeast2，代码行数:41，代码来源:UncorrelatedRates.java

示例12: branchLogP

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
@Override
public double branchLogP(int speciesTreeNodeNumber, Node speciesTreeNode, double ploidy, double[] branchCoalescentTimes, int branchLineageCount, int branchEventCount) {
    final RealParameter popSizes = popSizesInput.get();
    final double popSize = popSizes.getValue(speciesTreeNodeNumber);
    double logP = constantLogP(popSize, ploidy, branchCoalescentTimes, branchLineageCount, branchEventCount);

    return logP;
}
开发者ID:genomescale，项目名称:starbeast2，代码行数:9，代码来源:ConstantPopulations.java

示例13: serialize

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
@Override
public void serialize(Node speciesTreeNode, StringBuffer buf, DecimalFormat df) {
    final RealParameter popSizes = popSizesInput.get();
    final int speciesTreeNodeNumber = speciesTreeNode.getNr();
    final double branchPopSize = popSizes.getValue(speciesTreeNodeNumber);

    buf.append("dmv={");
    if (df == null) {
        buf.append(branchPopSize);
    } else {
        buf.append(df.format(branchPopSize));
    }
    buf.append("}");
}
开发者ID:genomescale，项目名称:starbeast2，代码行数:15，代码来源:ConstantPopulations.java

示例14: randomInit

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
private void randomInit(final SpeciesTree speciesTree, List<MRCAPrior> calibrations) {
	final RealParameter birthRateParameter = birthRate.get();
	final Double lambda = (birthRateParameter == null) ? 1.0 : birthRateParameter.getValue();
	final Double initialPopSize = 1.0 / lambda; // scales coalescent tree height inverse to birth rate
	final RealParameter popSize = new RealParameter(initialPopSize.toString());
    final ConstantPopulation pf = new ConstantPopulation();
    pf.setInputValue("popSize", popSize);

    final RandomTree rnd = new RandomTree();
    rnd.setInputValue("taxonset", speciesTree.getTaxonset());
    if (speciesTree.hasDateTrait()) rnd.setInputValue("trait", speciesTree.getDateTrait());

    for (final MRCAPrior cal: calibrations) rnd.setInputValue("constraint", cal);

    rnd.setInputValue("populationModel", pf);
    rnd.setInputValue("populationModel", pf);
    rnd.initAndValidate();

    speciesTree.assignFromWithoutID(rnd);
    // System.out.println("BEFORE = " + speciesTree.toString());

    /*final TraitSet speciesTipDates = speciesTree.getDateTrait();
    if (speciesTree.hasDateTrait()) {
    	for (Node node: speciesTree.getNodesAsArray()) {
    		if (node.isLeaf()) {
    			final String taxonName = node.getID();
    			final double taxonHeight = speciesTipDates.getValue(taxonName);
    			node.setHeight(taxonHeight);
    			
    		}
    	}
        System.out.println("AFTER = " + speciesTree.toString());
    }*/
}
开发者ID:genomescale，项目名称:starbeast2，代码行数:35，代码来源:StarBeastInitializer.java

示例15: proposal

import beast.core.parameter.RealParameter; //导入方法依赖的package包/类
/**
 * override this for proposals,
 * returns log of hastingRatio, or Double.NEGATIVE_INFINITY if proposal should not be accepted *
 */
@Override
public double proposal() {

    RealParameter param = parameterInput.get(this);

    int i = Randomizer.nextInt(param.getDimension());
    double value = param.getValue(i);
    double newValue = value;
    if (useGaussian) {
        newValue += Randomizer.nextGaussian() * windowSize;
    } else {
        newValue += Randomizer.nextDouble() * 2 * windowSize - windowSize;
    }

    if (newValue < param.getLower() || newValue > param.getUpper()) {
        return Double.NEGATIVE_INFINITY;
    }
    if (newValue == value) {
        // this saves calculating the posterior
        return Double.NEGATIVE_INFINITY;
    }

    param.setValue(i, newValue);

    return 0.0;
}
开发者ID:CompEvol，项目名称:beast2，代码行数:31，代码来源:RealRandomWalkOperator.java


注：本文中的beast.core.parameter.RealParameter.getValue方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。