Package ubic.basecode.math

Class SpecFunc

java.lang.Object

ubic.basecode.math.SpecFunc

public class SpecFunc
extends Object

Assorted special functions, primarily concerning probability distributions. For cumBinomial use cern.jet.stat.Probability.binomial.

Mostly ported from the R source tree (dhyper.c etc.), much due to Catherine Loader.

Author:

Paul Pavlidis

See Also:

• cern.jet.stat.gamma
• cern.jet.math.arithmetic

Constructor Summary

Constructors

Constructor	Description
SpecFunc()

Method Summary

Modifier and Type	Method	Description
static double	dbinom(double x, double n, double p)	See dbinom_raw.
static double	dhyper(int x, int r, int b, int n)	Ported from R (Catherine Loader)
static double	phyper(int x, int NR, int NB, int n, boolean lowerTail)	Ported from R phyper.c
static double	trigammaInverse(double x)
static DoubleMatrix1D	trigammaInverse(DoubleMatrix1D x)	Ported from limma

Methods inherited from class java.lang.Object

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

Constructor Details

SpecFunc

public SpecFunc()

Method Details

dbinom

public static double dbinom(double x,
 double n,
 double p)

See dbinom_raw.

Parameters:

x - Number of successes

n - Number of trials

p - Probability of success

Returns:

dhyper

public static double dhyper(int x,
 int r,
 int b,
 int n)

Ported from R (Catherine Loader)

DESCRIPTION

Given a sequence of r successes and b failures, we sample n (\le b+r) items without replacement. The hypergeometric probability is the probability of x successes:

               choose(r, x) * choose(b, n-x)
 (x; r,b,n) =  -----------------------------  =
                     choose(r+b, n)

    dbinom(x,r,p) * dbinom(n-x,b,p)
 = --------------------------------
       dbinom(n,r+b,p)
 

for any p. For numerical stability, we take p=n/(r+b); with this choice, the denominator is not exponentially small.

phyper

public static double phyper(int x,
 int NR,
 int NB,
 int n,
 boolean lowerTail)

Ported from R phyper.c

Sample of n balls from NR red and NB black ones; x are red

Parameters:

x - - number of reds retrieved == successes

NR - - number of reds in the urn. == positives

NB - - number of blacks in the urn == negatives

n - - the total number of objects drawn == successes + failures

lowerTail -

Returns:

cumulative hypergeometric distribution.

trigammaInverse

public static double trigammaInverse(double x)

Parameters:

x -

Returns:

trigammaInverse

public static DoubleMatrix1D trigammaInverse(DoubleMatrix1D x)

Ported from limma

Parameters:

x - vector to be operated on

Returns:

solution for y: trigamma(y) = x