public final class MathUtil
extends Object

General math utilities

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class MathUtil.LogMath
A collection of common math operations that work with log values.

Field Summary

Fields
Modifier and Type	Field	Description
`static MathUtil.LogMath`	`LOG_10_MATH`
`static MathUtil.LogMath`	`LOG_2_MATH`
`static double`	`LOG_4_BASE_E`	Constant to convert between the natural base e and 4.0.
`static double`	`MAX_PROB_BELOW_ONE`	The double value closest to 1 while still being less than 1.
`static MathUtil.LogMath`	`NATURAL_LOG_MATH`

Method Summary

All Methods Static Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`static int`	`compare(int v1, int v2)`
`static double[]`	`divide(double[] numerators, double[] denominators)`	Calculates the ratio of two arrays of the same length.
`static double`	`divide(double numerator, double denominator)`	Divide two Doubles but return 0.0 if the denominator is 0
`static int`	`indexOfMax(double[] nums)`	Returns the index of the largest element in the array.
`static int`	`indexOfMax(long[] nums)`	Returns the index of the largest element in the array.
`static int`	`indexOfMin(double[] nums)`	Returns the index of the smallest element in the array.
`static int`	`indexOfMin(int[] nums)`	Returns the index of the smallest element in the array.
`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
`static double[]`	`logLikelihoodsToProbs(double[] likelihoods)`	Deprecated.
`static double`	`max(double[] nums)`	Returns the largest value stored in the array.
`static long`	`max(long[] nums)`	Returns the largest value stored in the array.
`static double`	`mean(double[] in, int start, int stop)`	Calculated the mean of an array of doubles.
`static double`	`median(double... in)`	Calculate the median of an array of doubles.
`static byte`	`min(byte[] nums)`	Returns the smallest value stored in the array.
`static double`	`min(double[] nums)`	Returns the smallest value stored in the array.
`static int`	`min(int[] nums)`	Returns the smallest value stored in the array.
`static short`	`min(short[] nums)`	Returns the smallest value stored in the array.
`static double[]`	`multiply(double[] lhs, double[] rhs)`	Calculates the product of two arrays of the same length.
`static Double`	`percentageOrNull(Long numerator, Long denominator)`	Obtains percentage of two Longs
`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.
`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.
`static double[]`	`promote(int[] is)`	"Promotes" an int[] into a double array with the same values (or as close as precision allows).
`static double`	`round(double num, int precision)`	Round off the value to the specified precision.
`static double[]`	`seq(double from, double to, double by)`	Mimic's R's seq() function to produce a sequence of equally spaced numbers.
`static double`	`stddev(double[] in, int start, int length)`	Calculated the standard deviation of an array of doubles.
`static double`	`stddev(double[] in, int start, int stop, double mean)`	Calculated the standard deviation of an array of doubles.
`static double`	`sum(double[] arr)`	Returns the sum of the elements in the array.
`static double[]`	`sum(double[] lhs, double[] rhs)`	calculates the sum of the arrays as a third array.
`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.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - MAX_PROB_BELOW_ONE
```
public static final double MAX_PROB_BELOW_ONE
```
    The double value closest to 1 while still being less than 1.
    
    See Also:
    
    Constant Field Values
  - LOG_4_BASE_E
```
public static final double LOG_4_BASE_E
```
    Constant to convert between the natural base e and 4.0. Useful for entropy calculations on DNA.
  - LOG_2_MATH
```
public static final MathUtil.LogMath LOG_2_MATH
```
  - NATURAL_LOG_MATH
```
public static final MathUtil.LogMath NATURAL_LOG_MATH
```
  - LOG_10_MATH
```
public static final MathUtil.LogMath LOG_10_MATH
```
- Method Detail
  - 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.
  - 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.
  - 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.
  - 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.
  - 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.
  - 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.
  - 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[] 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.

Class MathUtil

Nested Class Summary

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MAX_PROB_BELOW_ONE

LOG_4_BASE_E

LOG_2_MATH

NATURAL_LOG_MATH

LOG_10_MATH

Method Detail

log10_1p

mean

stddev

stddev

compare

median

percentageOrNull

round

divide

max

indexOfMax

max

indexOfMax

min

min

min

min

indexOfMin

indexOfMin

seq

promote

logLikelihoodsToProbs

pNormalizeLogProbability

divide

pNormalizeVector

multiply

sum

sum

sum