Example usage for java.lang Math log1p

Introduction

In this page you can find the example usage for java.lang Math log1p.

Prototype

public static double log1p(double x) 

Source Link

Document

Returns the natural logarithm of the sum of the argument and 1.

Usage

From source file:Main.java

public static void main(String[] args) {
    double x = 123456.7;
    double y = -123.45;

    // call log1p and print the result
    System.out.println("Math.log1p(" + x + ")=" + Math.log1p(x));

    // call log1p and print the result
    System.out.println("Math.log1p(" + y + ")=" + Math.log1p(y));

}

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From source file:bide.prior.PriorBeta.java

public static double logPdf(double x, double alpha, double beta) {

    double z = recomputeZ(alpha, beta);

    double logX = Math.log(x);
    double log1mX = Math.log1p(-x);
    return ((alpha - 1) * logX + (beta - 1) * log1mX - z);
}

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From source file:bide.prior.PriorBeta.java

public static double pdf(double x, double alpha, double beta) {
    double z = recomputeZ(alpha, beta);

    double logX = Math.log(x);
    double log1mX = Math.log1p(-x);
    return Math.exp((alpha - 1) * logX + (beta - 1) * log1mX - z);

}

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From source file:edu.umd.umiacs.clip.tools.scor.BM25Scorer.java

protected final float idf(float df) {
    return (float) Math.log1p((N - df + 0.5) / (df + 0.5));
}

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From source file:beast.math.distributions.BetaDistribution.java

/**
 * probability density function of the distribution
 *
 * @param x argument//from w w w.j a  v  a 2 s.co  m
 * @return pdf value
 */
public double pdf(double x) {
    recomputeZ();
    if (x < 0 || x > 1) {
        return 0;
    } else if (x == 0) {
        if (alpha < 1) {
            // AR - throwing exceptions deep in numerical code causes trouble. Catching runtime
            // exceptions is bad. Better to return NaN and let the calling code deal with it.
            return Double.NaN;
            //                throw MathRuntimeException.createIllegalArgumentException(
            //                        "Cannot compute beta density at 0 when alpha = {0,number}", alpha);
        }
        return 0;
    } else if (x == 1) {
        if (beta < 1) {
            // AR - throwing exceptions deep in numerical code causes trouble. Catching runtime
            // exceptions is bad. Better to return NaN and let the calling code deal with it.
            return Double.NaN;
            //                throw MathRuntimeException.createIllegalArgumentException(
            //                        "Cannot compute beta density at 1 when beta = %.3g", beta);
        }
        return 0;
    } else {
        double logX = Math.log(x);
        double log1mX = Math.log1p(-x);
        return Math.exp((alpha - 1) * logX + (beta - 1) * log1mX - z);
    }
}

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From source file:beast.math.distributions.BetaDistribution.java

/**
 * the natural log of the probability density function of the distribution
 *
 * @param x argument/* www .  j a v  a2s  .c om*/
 * @return log pdf value
 */
public double logPdf(double x) {
    recomputeZ();
    if (x < 0 || x > 1) {
        return 0;
    } else if (x == 0) {
        if (alpha < 1) {
            // AR - throwing exceptions deep in numerical code causes trouble. Catching runtime
            // exceptions is bad. Better to return NaN and let the calling code deal with it.
            return Double.NaN;
            //                throw MathRuntimeException.createIllegalArgumentException(
            //                        "Cannot compute beta density at 0 when alpha = {0,number}", alpha);
        }
        return 0;
    } else if (x == 1) {
        if (beta < 1) {
            // AR - throwing exceptions deep in numerical code causes trouble. Catching runtime
            // exceptions is bad. Better to return NaN and let the calling code deal with it.
            return Double.NaN;
            //                throw MathRuntimeException.createIllegalArgumentException(
            //                        "Cannot compute beta density at 1 when beta = %.3g", beta);
        }
        return 0;
    } else {
        double logX = Math.log(x);
        double log1mX = Math.log1p(-x);
        return (alpha - 1) * logX + (beta - 1) * log1mX - z;
    }
}

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From source file:dr.math.distributions.BetaDistribution.java

/**
 * the natural log of the probability density function of the distribution
 *
 * @param x argument//  ww w  . j av a  2 s.  com
 * @return log pdf value
 */
public double logPdf(double x) {
    recomputeZ();
    if (x < 0 || x > 1) {
        return Double.NEGATIVE_INFINITY;
    } else if (x == 0) {
        if (alpha < 1) {
            // AR - throwing exceptions deep in numerical code causes trouble. Catching runtime
            // exceptions is bad. Better to return NaN and let the calling code deal with it.
            return Double.NaN;
            //                throw MathRuntimeException.createIllegalArgumentException(
            //                        "Cannot compute beta density at 0 when alpha = {0,number}", alpha);
        }
        if (alpha == 1) {
            return 0;
        }
        return Double.NEGATIVE_INFINITY;
    } else if (x == 1) {
        if (beta < 1) {
            // AR - throwing exceptions deep in numerical code causes trouble. Catching runtime
            // exceptions is bad. Better to return NaN and let the calling code deal with it.
            return Double.NaN;
            //                throw MathRuntimeException.createIllegalArgumentException(
            //                        "Cannot compute beta density at 1 when beta = %.3g", beta);
        }
        if (beta == 1) {
            return 0;
        }
        return Double.NEGATIVE_INFINITY;
    } else {
        double logX = Math.log(x);
        double log1mX = Math.log1p(-x);
        return (alpha - 1) * logX + (beta - 1) * log1mX - z;
    }
}

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From source file:edu.cornell.med.icb.goby.modes.TallyBasesMode.java

/**
 * Run the tally bases mode.//from  w w  w . ja v a  2 s .  c o m
 *
 * @throws java.io.IOException error reading / writing
 */
@Override
public void execute() throws IOException {
    if (basenames.length != 2) {
        System.err.println("Exactly two basenames are supported at this time.");
        System.exit(1);
    }
    final CountsArchiveReader[] archives = new CountsArchiveReader[basenames.length];
    int i = 0;
    for (final String basename : basenames) {
        archives[i++] = new CountsArchiveReader(basename, alternativeCountArhive);
    }

    final CountsArchiveReader archiveA = archives[0];
    final CountsArchiveReader archiveB = archives[1];
    // keep only common reference sequences between the two input count archives.
    final ObjectSet<String> identifiers = new ObjectOpenHashSet<String>();
    identifiers.addAll(archiveA.getIdentifiers());
    identifiers.retainAll(archiveB.getIdentifiers());
    // find the optimal offset A vs B:
    final int offset = offsetString.equals("auto") ? optimizeOffset(archiveA, archiveB, identifiers)
            : Integer.parseInt(offsetString);
    System.out.println("offset: " + offset);

    final RandomAccessSequenceCache cache = new RandomAccessSequenceCache();
    if (cache.canLoad(genomeCacheFilename)) {
        try {
            cache.load(genomeCacheFilename);
        } catch (ClassNotFoundException e) {
            System.err.println("Cannot load cache from disk. Consider deleting the cache and rebuilding.");
            e.printStackTrace();
            System.exit(1);
        }
    } else {
        Reader reader = null;
        try {
            if (genomeFilename.endsWith(".fa") || genomeFilename.endsWith(".fasta")) {
                reader = new FileReader(genomeFilename);
                cache.loadFasta(reader);
            } else if (genomeFilename.endsWith(".fa.gz") || genomeFilename.endsWith(".fasta.gz")) {
                reader = new InputStreamReader(new GZIPInputStream(new FileInputStream(genomeFilename)));
                cache.loadFasta(reader);
            } else {
                System.err.println("The format of the input file is not supported at this time.");
                System.exit(1);
            }
        } finally {
            IOUtils.closeQuietly(reader);
        }
    }

    System.out.println("Will use genome cache basename: " + genomeCacheFilename);
    cache.save(genomeCacheFilename);
    final Random random = new Random(new Date().getTime());

    final double delta = cutoff;
    final int countThreshold = 30;
    final PrintStream output = new PrintStream(outputFilename);
    writeHeader(output, windowSize);
    for (final String referenceSequenceId : identifiers) {
        if (isReferenceIncluded(referenceSequenceId)) {

            final int referenceIndex = cache.getReferenceIndex(referenceSequenceId);
            if (referenceIndex != -1) {
                // sequence in cache.
                System.out.println("Processing sequence " + referenceSequenceId);
                final double sumA = getSumOfCounts(archiveA.getCountReader(referenceSequenceId));
                final double sumB = getSumOfCounts(archiveB.getCountReader(referenceSequenceId));
                final int referenceSize = cache.getSequenceSize(referenceIndex);
                // process this sequence:
                final AnyTransitionCountsIterator iterator = new AnyTransitionCountsIterator(
                        archiveA.getCountReader(referenceSequenceId),
                        new OffsetCountsReader(archiveB.getCountReader(referenceSequenceId), offset));

                while (iterator.hasNextTransition()) {
                    iterator.nextTransition();
                    final int position = iterator.getPosition();
                    final int countA = iterator.getCount(0);
                    final int countB = iterator.getCount(1);

                    if (countA + countB >= countThreshold) {
                        final double foldChange = Math.log1p(countA) - Math.log1p(countB) - Math.log(sumA)
                                + Math.log(sumB);
                        if (foldChange >= delta || foldChange <= -delta) {
                            if (random.nextDouble() < sampleRate) {
                                tallyPosition(cache, referenceIndex, position, foldChange, windowSize,
                                        referenceSize, referenceSequenceId, output, countA, countB, sumA, sumB);
                            }
                        }
                    }
                }
                iterator.close();
            }
        }
        output.flush();
    }
    output.close();
}

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From source file:de.tudarmstadt.lt.ltbot.prefetch.DecesiveValuePrioritizer.java

int getPrecedenceCost(double val, int schedulingConstants_priority) {
    // cost should be in [0,_maxPrecedence], lower values are better, try to squash values into this range
    int cost = _maxPrecedence;
    switch (schedulingConstants_priority) {
    case SchedulingConstants.HIGHEST:
        return 1; // 2^0
    case SchedulingConstants.HIGH:
        return 4; // 2^2
    case SchedulingConstants.MEDIUM:
        return 8; // 2^3
    case SchedulingConstants.NORMAL:
        cost = 64; // 2^6
    }/*from w w w .  j  a  va 2 s.  c  o m*/

    // --> squeeze [_assignmentBoundaries[SchedulingConstants.NORMAL], _maxvalue] into [64, _maxPrecedence]
    //            [A, B] --> [a, b]
    //            newval = (val - A)*(b-a)/(B-A) + a

    double B = Math.min(Integer.MAX_VALUE, _maxvalue); // use maxvalue as maximum if specified and below Integer.maxvalue
    if (val >= B)
        return _maxPrecedence;
    // take log of A, B and val to make computation numerically more stable
    B = Math.log1p(B);
    double A = Math.log1p(_assignmentBoundaries[SchedulingConstants.MEDIUM]);
    val = Math.log1p(val);
    //      assert val >= A : "Value is smaller than lower boundary. That should not happen.";
    double a = cost;
    double b = _maxPrecedence;
    cost = (int) Math.ceil((val - A) * (b - a) / (B - A) + a);
    return cost;
}

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From source file:com.jaeksoft.searchlib.learning.StandardLearner.java

@Override
public void classify(String data, FieldMap sourceFieldMap, int maxRank, double minScore,
        Collection<LearnerResultItem> collector) throws IOException, SearchLibException {
    rwl.r.lock();/*from   www  .  java2 s.  co m*/
    try {
        Collection<TargetField> targetFields = checkIndex(sourceFieldMap);
        TreeMap<String, LearnerResultItem> targetMap = new TreeMap<String, LearnerResultItem>();
        fieldClassify(FIELD_SOURCE_DATA, null, data, targetMap);
        for (TargetField targetField : targetFields)
            fieldClassify(targetField.getBoostedName(), targetField.getBoost(), data, targetMap);
        for (LearnerResultItem learnerResultItem : targetMap.values()) {
            learnerResultItem.score = learnerResultItem.score / learnerResultItem.count
                    * Math.log1p(learnerResultItem.count);
            if (learnerResultItem.score > minScore)
                collector.add(learnerResultItem);
        }
    } finally {
        rwl.r.unlock();
    }
}

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