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OpenMS::Math Namespace Reference

Math namespace. More...

Classes

class  AsymmetricStatistics
 Internal class for asymmetric distributions. More...
 
class  AveragePosition
 Maintain an average position by summing up positions with weights. More...
 
class  BasicStatistics
 Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation. More...
 
class  BilinearInterpolation
 Provides access to bilinearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero. More...
 
class  GammaDistributionFitter
 Implements a fitter for the Gamma distribution. More...
 
class  GaussFitter
 Implements a fitter for gaussian functions. More...
 
class  GumbelDistributionFitter
 Implements a fitter for the Gumbel distribution. More...
 
class  Histogram
 Representation of a histogram. More...
 
class  LinearInterpolation
 Provides access to linearly interpolated values (and derivatives) from discrete data points. Values beyond the given range of data points are implicitly taken as zero. More...
 
class  LinearRegression
 This class offers functions to perform least-squares fits to a straight line model, $ Y(c,x) = c_0 + c_1 x $. More...
 
class  PosteriorErrorProbabilityModel
 Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture. More...
 
class  QuadraticRegression
 
class  ROCCurve
 ROCCurves show the trade-off in sensitivity and specificity for binary classifiers using different cutoff values. More...
 

Functions

static double ceilDecimal (double x, int decPow)
 rounds x up to the next decimal power 10 ^ decPow More...
 
static double roundDecimal (double x, int decPow)
 rounds x to the next decimal power 10 ^ decPow More...
 
static double intervalTransformation (double x, double left1, double right1, double left2, double right2)
 transforms point x of interval [left1,right1] into interval [left2,right2] More...
 
double linear2log (double x)
 Transforms a number from linear to log10 scale. Avoids negative logarithms by adding 1. More...
 
double log2linear (double x)
 Transforms a number from log10 to to linear scale. Subtracts the 1 added by linear2log(double) More...
 
bool isOdd (UInt x)
 Returns true if the given integer is odd. More...
 
template<typename T >
round (T x)
 Rounds the value. More...
 
static bool approximatelyEqual (double a, double b, double tol)
 Returns if a is approximately equal b , allowing a tolerance of tol. More...
 
template<typename T >
gcd (T a, T b)
 Returns the greatest common divisor (gcd) of two numbers by applying the Euclidean algorithm. More...
 
template<typename T >
gcd (T a, T b, T &u1, T &u2)
 Returns the greatest common divisor by applying the extended Euclidean algorithm (Knuth TAoCP vol. 2, p342). Calculates u1, u2 and u3 (which is returned) so that a * u1 + b * u2 = u3 = gcd(a, b, u1, u2) More...
 
template<typename ValueType , typename BinSizeType >
std::ostream & operator<< (std::ostream &os, const Histogram< ValueType, BinSizeType > &hist)
 Print the contents to a stream. More...
 
template<typename Iterator >
std::vector< Wm5::Vector2d > iteratorRange2Wm5Vectors (Iterator x_begin, Iterator x_end, Iterator y_begin)
 Copies the distance(x_begin,x_end) elements starting at x_begin and y_begin into the Wm5::Vector. More...
 
template<typename IteratorType >
static void checkIteratorsNotNULL (IteratorType begin, IteratorType end)
 Helper function checking if two iterators are not equal. More...
 
template<typename IteratorType >
static void checkIteratorsEqual (IteratorType begin, IteratorType end)
 Helper function checking if two iterators are equal. More...
 
template<typename IteratorType1 , typename IteratorType2 >
static void checkIteratorsAreValid (IteratorType1 begin_b, IteratorType1 end_b, IteratorType2 begin_a, IteratorType2 end_a)
 Helper function checking if an iterator and a co-iterator both have a next element. More...
 
template<typename IteratorType >
static double sum (IteratorType begin, IteratorType end)
 Calculates the sum of a range of values. More...
 
template<typename IteratorType >
static double mean (IteratorType begin, IteratorType end)
 Calculates the mean of a range of values. More...
 
template<typename IteratorType >
static double median (IteratorType begin, IteratorType end, bool sorted=false)
 Calculates the median of a range of values. More...
 
template<typename IteratorType >
static double quantile1st (IteratorType begin, IteratorType end, bool sorted=false)
 Calculates the first quantile of a range of values. More...
 
template<typename IteratorType >
static double quantile3rd (IteratorType begin, IteratorType end, bool sorted=false)
 Calculates the third quantile of a range of values. More...
 
template<typename IteratorType >
static double variance (IteratorType begin, IteratorType end, double mean=std::numeric_limits< double >::max())
 Calculates the variance of a range of values. More...
 
template<typename IteratorType >
static double sd (IteratorType begin, IteratorType end, double mean=std::numeric_limits< double >::max())
 Calculates the standard deviation of a range of values. More...
 
template<typename IteratorType >
static double absdev (IteratorType begin, IteratorType end, double mean=std::numeric_limits< double >::max())
 Calculates the absolute deviation of a range of values. More...
 
template<typename IteratorType1 , typename IteratorType2 >
static double covariance (IteratorType1 begin_a, IteratorType1 end_a, IteratorType2 begin_b, IteratorType2 end_b)
 Calculates the covariance of two ranges of values. More...
 
template<typename IteratorType1 , typename IteratorType2 >
static double meanSquareError (IteratorType1 begin_a, IteratorType1 end_a, IteratorType2 begin_b, IteratorType2 end_b)
 Calculates the mean square error for the values in [begin_a, end_a) and [begin_b, end_b) More...
 
template<typename IteratorType1 , typename IteratorType2 >
static double classificationRate (IteratorType1 begin_a, IteratorType1 end_a, IteratorType2 begin_b, IteratorType2 end_b)
 Calculates the classification rate for the values in [begin_a, end_a) and [begin_b, end_b) More...
 
template<typename IteratorType1 , typename IteratorType2 >
static double matthewsCorrelationCoefficient (IteratorType1 begin_a, IteratorType1 end_a, IteratorType2 begin_b, IteratorType2 end_b)
 Calculates the Matthews correlation coefficient for the values in [begin_a, end_a) and [begin_b, end_b) More...
 
template<typename IteratorType1 , typename IteratorType2 >
static double pearsonCorrelationCoefficient (IteratorType1 begin_a, IteratorType1 end_a, IteratorType2 begin_b, IteratorType2 end_b)
 Calculates the Pearson correlation coefficient for the values in [begin_a, end_a) and [begin_b, end_b) More...
 
template<typename Value >
static void computeRank (std::vector< Value > &w)
 Replaces the elements in vector w by their ranks. More...
 
template<typename IteratorType1 , typename IteratorType2 >
static double rankCorrelationCoefficient (IteratorType1 begin_a, IteratorType1 end_a, IteratorType2 begin_b, IteratorType2 end_b)
 calculates the rank correlation coefficient for the values in [begin_a, end_a) and [begin_b, end_b) More...
 

Detailed Description

Math namespace.

Contains mathematical auxiliary functions.

Function Documentation

static void OpenMS::Math::computeRank ( std::vector< Value > &  w)
static

Replaces the elements in vector w by their ranks.

Referenced by rankCorrelationCoefficient().

std::vector<Wm5::Vector2d> OpenMS::Math::iteratorRange2Wm5Vectors ( Iterator  x_begin,
Iterator  x_end,
Iterator  y_begin 
)

Copies the distance(x_begin,x_end) elements starting at x_begin and y_begin into the Wm5::Vector.

Referenced by LinearRegression::computeRegression(), QuadraticRegression::computeRegressionWeighted(), and LinearRegression::computeRegressionWeighted().

std::ostream& OpenMS::Math::operator<< ( std::ostream &  os,
const Histogram< ValueType, BinSizeType > &  hist 
)

Print the contents to a stream.


OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:47 using doxygen 1.8.9.1