com.compomics.util.math

Class BasicMathFunctions

java.lang.Object

com.compomics.util.math.BasicMathFunctions

public class BasicMathFunctions
extends Object

Class used to perform basic mathematical functions.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
BasicMathFunctions()

Method Summary

Methods

Modifier and Type	Method and Description
static int	factorial(int n) Returns n!
static double	getCombination(int k, int n) Returns the number of k-combinations in a set of n elements.
static double	getCorrelation(ArrayList<Double> series1, ArrayList<Double> series2) Returns the population Pearson correlation r between series1 and series2.
static double	getRobustCorrelation(ArrayList<Double> series1, ArrayList<Double> series2) Returns the population Pearson correlation r between series1 and series2.
static double	mad(double[] ratios) Method estimating the median absolute deviation.
static double	mean(ArrayList<Double> input) Convenience method returning the mean of a list of doubles.
static double	median(ArrayList<Double> input) Method to estimate the median.
static double	median(double[] ratios) Method to estimate the median.
static double	percentile(ArrayList<Double> input, double percentile) Returns the desired percentile in a given list of double.
static double	percentile(double[] input, double percentile) Returns the desired percentile in a given array of double.
static double	std(ArrayList<Double> input) Convenience method returning the standard deviation of a list of doubles.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BasicMathFunctions

public BasicMathFunctions()

Method Detail

factorial

public static int factorial(int n)

Returns n!

Parameters:

n - a given integer

Returns:

the corresponding factorial

getCombination

public static double getCombination(int k,
                    int n)

Returns the number of k-combinations in a set of n elements.

Parameters:

k - the number of k-combinations

n - the number of elements

Returns:

the number of k-combinations in a set of n elements

median

public static double median(double[] ratios)

Method to estimate the median.

Parameters:

ratios - array of double

Returns:

median of the input

median

public static double median(ArrayList<Double> input)

Method to estimate the median.

Parameters:

input - ArrayList of double

Returns:

median of the input

percentile

public static double percentile(double[] input,
                double percentile)

Returns the desired percentile in a given array of double. If the percentile is between two values a linear interpolation is done.

Parameters:

input - the input array

percentile - the desired percentile. 0.01 returns the first percentile. 0.5 returns the median.

Returns:

the desired percentile

percentile

public static double percentile(ArrayList<Double> input,
                double percentile)

Returns the desired percentile in a given list of double. If the percentile is between two values a linear interpolation is done.

Parameters:

input - the input list

percentile - the desired percentile. 0.01 returns the first percentile. 0.5 returns the median.

Returns:

the desired percentile

mad

public static double mad(double[] ratios)

Method estimating the median absolute deviation.

Parameters:

ratios - array of doubles

Returns:

the mad of the input

std

public static double std(ArrayList<Double> input)

Convenience method returning the standard deviation of a list of doubles. Returns 0 if the list is null or of size < 2.

Parameters:

input - input list

Returns:

the corresponding standard deviation

mean

public static double mean(ArrayList<Double> input)

Convenience method returning the mean of a list of doubles.

Parameters:

input - input list

Returns:

the corresponding mean

getCorrelation

public static double getCorrelation(ArrayList<Double> series1,
                    ArrayList<Double> series2)

Returns the population Pearson correlation r between series1 and series2.

Parameters:

series1 - first series to compare

series2 - second series to compare

Returns:

the Pearson correlation factor

getRobustCorrelation

public static double getRobustCorrelation(ArrayList<Double> series1,
                          ArrayList<Double> series2)

Returns the population Pearson correlation r between series1 and series2. Here the correlation factor is estimated using median and percentile distance instead of mean and standard deviation.

Parameters:

series1 - the first series to inspect

series2 - the second series to inspect

Returns:

a robust version of the Pearson correlation factor