Class MathUtil

Method Details

• log10_1p

  public static double log10_1p(double x)

  this function mimics the behavior of log_1p but resulting in log _base 10_ of (1+x) instead of natural log of 1+x

• mean

  public static double mean(double[] in, int start, int stop)

  Calculated the mean of an array of doubles.

• mean

  public static double mean(double[] in)

• stddev

  public static double stddev(double[] in, int start, int length)

  Calculated the standard deviation of an array of doubles.

• stddev

  public static double stddev(double[] in, int start, int stop, double mean)

  Calculated the standard deviation of an array of doubles.

• stddev

  public static double stddev(double[] in, double mean)

  Calculated the standard deviation of an array of doubles.

• compare

  public static int compare(int v1, int v2)

• median

  public static double median(double... in)

  Calculate the median of an array of doubles. Assumes that the input is sorted

• percentageOrNull

  public static Double percentageOrNull(Long numerator, Long denominator)

  Obtains percentage of two Longs

  Parameters:

  numerator - dividend

  denominator - divisor

  Returns:

  numerator/(double)denominator if both are non-null and denominator != 0, else returns null.

• round

  public static double round(double num, int precision)

  Round off the value to the specified precision.

• divide

  public static double divide(double numerator, double denominator)

  Divide two Doubles but return 0.0 if the denominator is 0

  Parameters:

  numerator - dividend

  denominator - divisor

  Returns:

  numerator/denominator unless denominator is 0, in which case returns 0

• max

  public static double max(double[] nums)

  Returns the largest value stored in the array.

• capFromBelow

  public static double[] capFromBelow(double[] nums, double floor)

  Returns the array capped (from below) by the value of floor

• indexOfMax

  public static int indexOfMax(double[] nums)

  Returns the index of the largest element in the array. If there are multiple equal maxima then the earliest one in the array is returned.

• max

  public static long max(long[] nums)

  Returns the largest value stored in the array.

• indexOfMax

  public static int indexOfMax(long[] nums)

  Returns the index of the largest element in the array. If there are multiple equal maxima then the earliest one in the array is returned.

• subtractMax

  public static double[] subtractMax(double[] logLikelihoods)

• min

  public static double min(double[] nums)

  Returns the smallest value stored in the array.

• min

  public static int min(int[] nums)

  Returns the smallest value stored in the array.

• min

  public static short min(short[] nums)

  Returns the smallest value stored in the array.

• min

  public static byte min(byte[] nums)

  Returns the smallest value stored in the array.

• capFromAbove

  public static double[] capFromAbove(double[] nums, double top)

  Returns the array capped (from above) by the value of top

• indexOfMin

  public static int indexOfMin(int[] nums)

  Returns the index of the smallest element in the array. If there are multiple equal minima then the earliest one in the array is returned.

• indexOfMin

  public static int indexOfMin(double[] nums)

  Returns the index of the smallest element in the array. If there are multiple equal minima then the earliest one in the array is returned.

• seq

  public static double[] seq(double from, double to, double by)

  Mimic's R's seq() function to produce a sequence of equally spaced numbers.

• promote

  public static double[] promote(int[] is)

  "Promotes" an int[] into a double array with the same values (or as close as precision allows).

• logLikelihoodsToProbs

  @Deprecated public static double[] logLikelihoodsToProbs(double[] likelihoods)

  Deprecated.

• getProbabilityFromLog

  public static double[] getProbabilityFromLog(double[] lLikelihood)

  Takes a complete set of mutually exclusive logLikelihoods and converts them to probabilities with no rescaling. Will throw if underflow is detected (if all the likelihoods are less than -300)

• getLogFromProbability

  public static double[] getLogFromProbability(double[] likelihood)

  Takes a complete set of mutually exclusive Likelihoods and converts them to logLikelihoods.

• pNormalizeLogProbability

  public static double[] pNormalizeLogProbability(double[] lPosterior)

  Takes a complete set of mutually exclusive logPosteriors and converts them to probabilities that sum to 1 with as much fidelity as possible. Limits probabilities to be in the space: 0.9999999999999999 >= p >= (1-0.9999999999999999)/(lPosteriors.length-1)

• divide

  public static double[] divide(double[] numerators, double[] denominators)

  Calculates the ratio of two arrays of the same length.

• pNormalizeVector

  public static double[] pNormalizeVector(double[] pPosterior)

  Takes a vector of numbers and converts it to a vector of probabilities that sum to 1 with as much fidelity as possible. Limits probabilities to be in the space: 0.9999999999999999 >= p >= (1-0.9999999999999999)/(likelihoods.length-1)

• multiply

  public static double[] multiply(double[] lhs, double[] rhs)

  Calculates the product of two arrays of the same length.

• sum

  public static double[] sum(double[] lhs, double[] rhs)

  calculates the sum of the arrays as a third array.

• sum

  public static double[] sum(double[] lhs, double rhs)

  calculates the sum of an array and a double.

• sum

  public static double sum(double[] arr)

  Returns the sum of the elements in the array.

• sum

  public static long sum(long[] arr, int start, int stop)

  Returns the sum of the elements in the array starting with start and ending before stop.

• round

  public static long[] round(double... input)

  returns a long array containing the rounded values of the input array

• klDivergance

  public static double klDivergance(double[] measured, double[] distribution)

  Calculate the KL divergence from measured to distribution // https://en.wikipedia.org/wiki/Kullback%E2%80%93Leibler_divergence

• permute

  public static double[] permute(double[] array, org.apache.commons.math3.random.RandomDataGenerator rdg)

  permute the input array randomly (using a RandomDataGenerator)

  Parameters:

  array - input array

  rdg - a RandomDataGenerator for drawing a permutation from

  Returns:

  a newly allocated array with a permuted version of the original data.

• randomSublist

  public static <T> List<T> randomSublist(List<T> list, int n, Random random)

  A small utility function to choose n random elements (un-shuffled) from a list

  Parameters:

  list - A list of elements

  n - a number of elements requested from list

  random - a Random object to use for subsetting

  Returns:

  a list of n randomly chosen (but in the original order) elements from list. If the list has less than n elements it is returned in its entirety.