Java Code Examples for org.apache.commons.math3.stat.descriptive.DescriptiveStatistics#getN()

@Override
public Object doWork(Object first, Object second) throws IOException{
  if(null == first){
    throw new IOException(String.format(Locale.ROOT,"Invalid expression %s - null found for the first value",toExpression(constructingFactory)));
  }
  if(null == second){
    throw new IOException(String.format(Locale.ROOT,"Invalid expression %s - null found for the second value",toExpression(constructingFactory)));
  }
  if(!(first instanceof List<?>)){
    throw new IOException(String.format(Locale.ROOT,"Invalid expression %s - found type %s for the first value, expecting a List",toExpression(constructingFactory), first.getClass().getSimpleName()));
  }
  if(!(second instanceof Number)){
    throw new IOException(String.format(Locale.ROOT,"Invalid expression %s - found type %s for the second value, expecting a Number",toExpression(constructingFactory), first.getClass().getSimpleName()));
  }

  List<?> values = (List<?>)first;
  int window = ((Number)second).intValue();

  List<Number> moving = new ArrayList<>();
  DescriptiveStatistics slider = new DescriptiveStatistics(window);
  for(Object value : values){
    slider.addValue(((Number)value).doubleValue());
    if(slider.getN() >= window){
      double[] doubles = slider.getValues();
      double mean = slider.getMean();
      double total = 0;
      for(double d : doubles) {
        total+=Math.abs(d-mean);
      }
      moving.add(total/window);
    }
  }

  return moving;
}
 

/**
 * Calculates the average GPA for the course
 *
 * This is only applicable if Grade Points is the grading schema in use. However this is not currently checked.
 *
 * @return String average GPA
 */
private String getAverageGPA(final DescriptiveStatistics stats) {

	if (!StringUtils.equals(this.gradingSchemaName, "Grade Points")) {
		return null;
	}

	if (this.bottomPercents == null || this.bottomPercents.isEmpty()) {
		// cannot display averageGpa without bottomPercents
		return null;
	}

	if (stats.getN() == 0) {
		return "-";
	}

	// get all of the non null mapped grades
	// mapped grades will be null if the student doesn't have a course grade yet.
	final List<String> mappedGrades = this.courseGradeMap.values().stream().filter(c -> c.getMappedGrade() != null)
			.map(c -> (c.getMappedGrade())).collect(Collectors.toList());
	Double averageGPA = 0.0;
	for (final String mappedGrade : mappedGrades) {
		final Double grade = this.bottomPercents.get(mappedGrade);
		if (grade != null) {
			averageGPA += grade;
		} else {
			log.debug("Grade skipped when calculating course average GPA: {}. Calculated value will be incorrect.", mappedGrade);
		}
	}
	averageGPA /= mappedGrades.size();

	return String.format("%.2f", averageGPA);
}
 

@Override
public Map<String, Object> annotate(final ReferenceContext ref,
                                    final VariantContext vc,
                                    final AlleleLikelihoods<GATKRead, Allele> likelihoods) {
    Utils.nonNull(vc);
    if ( ! vc.hasGenotypes() ) {
        return Collections.emptyMap();
    }

    final Map<String,Object> returnMap = new LinkedHashMap<>();
    returnMap.put(GATKVCFConstants.NOCALL_CHROM_KEY, vc.getNoCallCount());

    final DescriptiveStatistics stats = new DescriptiveStatistics();
    for( final Genotype g : vc.getGenotypes() ) {
        if( g.hasGQ() ) {
            stats.addValue(g.getGQ());
        }
    }
    if( stats.getN() > 0L ) {
        returnMap.put(GATKVCFConstants.GQ_MEAN_KEY, String.format("%.2f", stats.getMean()));
        if( stats.getN() > 1L ) {
            returnMap.put(GATKVCFConstants.GQ_STDEV_KEY, String.format("%.2f", stats.getStandardDeviation()));
        }
    }

    return returnMap;
}
 

/**
 * Compute phi for the specified node id.
 *
 * @return phi value
 */
public double phi() {
  long latestHeartbeat = history.latestHeartbeatTime();
  DescriptiveStatistics samples = history.samples();
  if (samples.getN() < minSamples) {
    return 0.0;
  }
  return computePhi(samples, latestHeartbeat, System.currentTimeMillis());
}
 

/**
 * Computes the timeout for the next request.
 *
 * @param type the message type
 * @return the computed timeout for the next request
 */
private long computeTimeoutMillis(String type) {
  DescriptiveStatistics samples = replySamples.get(type);
  if (samples == null || samples.getN() < MIN_SAMPLES) {
    return MAX_TIMEOUT_MILLIS;
  }
  return Math.min(Math.max((int) samples.getMax() * TIMEOUT_FACTOR, MIN_TIMEOUT_MILLIS), MAX_TIMEOUT_MILLIS);
}
 

/**
 * Calculates the average GPA for the course
 *
 * This is only applicable if Grade Points is the grading schema in use. However this is not currently checked.
 *
 * @return String average GPA
 */
private String getAverageGPA(final DescriptiveStatistics stats) {

	if (!StringUtils.equals(this.gradingSchemaName, "Grade Points")) {
		return null;
	}

	if (this.bottomPercents == null || this.bottomPercents.isEmpty()) {
		// cannot display averageGpa without bottomPercents
		return null;
	}

	if (stats.getN() == 0) {
		return "-";
	}

	// get all of the non null mapped grades
	// mapped grades will be null if the student doesn't have a course grade yet.
	final List<String> mappedGrades = this.courseGradeMap.values().stream().filter(c -> c.getMappedGrade() != null)
			.map(c -> (c.getMappedGrade())).collect(Collectors.toList());
	Double averageGPA = 0.0;
	for (final String mappedGrade : mappedGrades) {
		final Double grade = this.bottomPercents.get(mappedGrade);
		if (grade != null) {
			averageGPA += grade;
		} else {
			log.debug("Grade skipped when calculating course average GPA: {}. Calculated value will be incorrect.", mappedGrade);
		}
	}
	averageGPA /= mappedGrades.size();

	return String.format("%.2f", averageGPA);
}
 

@Override
public Object doWork(Object first, Object second) throws IOException{
  if(null == first){
    throw new IOException(String.format(Locale.ROOT,"Invalid expression %s - null found for the first value",toExpression(constructingFactory)));
  }
  if(null == second){
    throw new IOException(String.format(Locale.ROOT,"Invalid expression %s - null found for the second value",toExpression(constructingFactory)));
  }
  if(!(first instanceof List<?>)){
    throw new IOException(String.format(Locale.ROOT,"Invalid expression %s - found type %s for the first value, expecting a List",toExpression(constructingFactory), first.getClass().getSimpleName()));
  }
  if(!(second instanceof Number)){
    throw new IOException(String.format(Locale.ROOT,"Invalid expression %s - found type %s for the second value, expecting a Number",toExpression(constructingFactory), first.getClass().getSimpleName()));
  }

  List<?> values = (List<?>)first;
  int window = ((Number)second).intValue();

  List<Number> moving = new ArrayList<>();
  DescriptiveStatistics slider = new DescriptiveStatistics(window);
  Percentile percentile = new Percentile();
  for(Object value : values){
    slider.addValue(((Number)value).doubleValue());
    if(slider.getN() >= window){
      double median = percentile.evaluate(slider.getValues(), 50);
      moving.add(median);
    }
  }

  return moving;
}
 

@Override
public Object doWork(Object first, Object second) throws IOException{
  if(null == first){
    throw new IOException(String.format(Locale.ROOT,"Invalid expression %s - null found for the first value",toExpression(constructingFactory)));
  }
  if(null == second){
    throw new IOException(String.format(Locale.ROOT,"Invalid expression %s - null found for the second value",toExpression(constructingFactory)));
  }
  if(!(first instanceof List<?>)){
    throw new IOException(String.format(Locale.ROOT,"Invalid expression %s - found type %s for the first value, expecting a List",toExpression(constructingFactory), first.getClass().getSimpleName()));
  }
  if(!(second instanceof Number)){
    throw new IOException(String.format(Locale.ROOT,"Invalid expression %s - found type %s for the second value, expecting a Number",toExpression(constructingFactory), first.getClass().getSimpleName()));
  }
  
  List<?> values = (List<?>)first;
  int window = ((Number)second).intValue();
  
  List<Number> moving = new ArrayList<>();
  DescriptiveStatistics slider = new DescriptiveStatistics(window);
  for(Object value : values){
    slider.addValue(((Number)value).doubleValue());
    
    if(slider.getN() >= window){
      moving.add(slider.getMean());
    }      
  }
  
  return moving;
}
 

@Override
public A getAction(final N node, final Map<A, N> actionsWithSuccessors) throws ActionPredictionFailedException {

	/* determine number of visits of the child with least visits */
	Entry<A, N> actionAndChildWithLeastVisits = null;
	Entry<A, N> actionAndChildWithBestVisit = null;
	int numOfVisitsOfThatChild = Integer.MAX_VALUE;
	double bestChildScore = Double.MAX_VALUE;
	for (Entry<A, N> child : actionsWithSuccessors.entrySet()) {
		DescriptiveStatistics observations = this.observationsPerNode.computeIfAbsent(child.getValue(), n -> new DescriptiveStatistics());
		int numOfVisitsOfThisChild = (int)observations.getN();
		if (numOfVisitsOfThisChild < numOfVisitsOfThatChild) {
			actionAndChildWithLeastVisits = child;
			numOfVisitsOfThatChild = numOfVisitsOfThisChild;
		}
		double bestScoreOfThisChild = this.metric.applyAsDouble(observations);
		if (bestScoreOfThisChild < bestChildScore) {
			bestChildScore = bestScoreOfThisChild;
			actionAndChildWithBestVisit = child;
		}
	}

	/* now decide */
	Objects.requireNonNull(actionAndChildWithLeastVisits);
	Objects.requireNonNull(actionAndChildWithBestVisit);
	if (numOfVisitsOfThatChild < this.k) {
		return actionAndChildWithLeastVisits.getKey();
	} else {
		return actionAndChildWithBestVisit.getKey();
	}
}
 

/**
 * Computes the phi value from the given samples.
 * <p>
 * The original phi value in Hayashibara's paper is calculated based on a normal distribution.
 * Here, we calculate it based on an exponential distribution.
 *
 * @param samples       the samples from which to compute phi
 * @param lastHeartbeat the last heartbeat
 * @param currentTime   the current time
 * @return phi
 */
private double computePhi(DescriptiveStatistics samples, long lastHeartbeat, long currentTime) {
  long size = samples.getN();
  long t = currentTime - lastHeartbeat;
  return (size > 0)
      ? phiFactor * t / samples.getMean()
      : 100;
}
 

/**
 * Calculates the mean for the set
 *
 * @return String mean
 */
protected final String getMean(final DescriptiveStatistics stats) {
	return stats.getN() > 0 ? String.format("%.2f", stats.getMean()) : "-";
}
 

/**
 * Calculates the median for the set
 *
 * @return String median
 */
protected final String getMedian(final DescriptiveStatistics stats) {
	return stats.getN() > 0 ? String.format("%.2f", stats.getPercentile(50)) : "-";
}
 

/**
 * Calculates the min for the set
 *
 * @return String min
 */
protected final String getMin(final DescriptiveStatistics stats) {
	return stats.getN() > 0 ? String.format("%.2f", stats.getMin()) : "-";
}
 

/**
 * Calculates the max for the set
 *
 * @return String max
 */
protected final String getMax(final DescriptiveStatistics stats) {
	return stats.getN() > 0 ? String.format("%.2f", stats.getMax()) : "-";
}
 

/**
 * Calculates the standard deviation for the set
 *
 * @return String standard deviation
 */
protected final String getStandardDeviation(final DescriptiveStatistics stats) {
	return stats.getN() > 0 ? String.format("%.2f", stats.getStandardDeviation()) : "-";
}
 

/**
 * Calculates the mean for the set
 *
 * @return String mean
 */
protected final String getMean(final DescriptiveStatistics stats) {
	return stats.getN() > 0 ? String.format("%.2f", stats.getMean()) : "-";
}
 

/**
 * Calculates the median for the set
 *
 * @return String median
 */
protected final String getMedian(final DescriptiveStatistics stats) {
	return stats.getN() > 0 ? String.format("%.2f", stats.getPercentile(50)) : "-";
}
 

/**
 * Calculates the min for the set
 *
 * @return String min
 */
protected final String getMin(final DescriptiveStatistics stats) {
	return stats.getN() > 0 ? String.format("%.2f", stats.getMin()) : "-";
}
 

/**
 * Calculates the max for the set
 *
 * @return String max
 */
protected final String getMax(final DescriptiveStatistics stats) {
	return stats.getN() > 0 ? String.format("%.2f", stats.getMax()) : "-";
}
 

/**
 * Calculates the standard deviation for the set
 *
 * @return String standard deviation
 */
protected final String getStandardDeviation(final DescriptiveStatistics stats) {
	return stats.getN() > 0 ? String.format("%.2f", stats.getStandardDeviation()) : "-";
}