The core class of a multivariate analysis. More...

#include <Bpp/Numeric/Stat/Mva/DualityDiagram.h>

Inheritance diagram for bpp::DualityDiagram:

Collaboration diagram for bpp::DualityDiagram:

Public Member Functions
	DualityDiagram ()
	Build an empty DualityDiagram object. More...

	DualityDiagram (const Matrix< double > &matrix, const std::vector< double > &rowWeights, const std::vector< double > &colWeights, unsigned int nbAxes, double tol=0.0000001, bool verbose=true) throw (Exception)
	Build a new DualityDiagram object. More...

virtual	~DualityDiagram ()

DualityDiagram *	clone () const
	Create a copy of this object and send a pointer to it. More...

void	setData (const Matrix< double > &matrix, const std::vector< double > &rowWeights, const std::vector< double > &colWeights, unsigned int nbAxes, double tol=0.0000001, bool verbose=true) throw (Exception)
	Set the data and perform computations. More...

std::vector< double >	computeVariancePercentagePerAxis () throw (Exception)

size_t	getNbOfKeptAxes () const throw (Exception)

const std::vector< double >	getRowWeights () const throw (Exception)

const std::vector< double >	getColumnWeights () const throw (Exception)

const std::vector< double > &	getEigenValues () const throw (Exception)

const RowMatrix< double > &	getRowCoordinates () const throw (Exception)

const RowMatrix< double > &	getColCoordinates () const throw (Exception)

const RowMatrix< double > &	getPrincipalAxes () const throw (Exception)

const RowMatrix< double > &	getPrincipalComponents () const throw (Exception)

Private Member Functions
void	check_ (const Matrix< double > &matrix, const std::vector< double > &rowWeights, const std::vector< double > &colWeights, unsigned int nbAxes) throw (Exception)

void	compute_ (const Matrix< double > &matrix, double tol, bool verbose)

Private Attributes
std::vector< double >	rowWeights_

std::vector< double >	colWeights_

size_t	nbAxes_

std::vector< double >	eigenValues_

RowMatrix< double >	eigenVectors_

RowMatrix< double >	rowCoord_

RowMatrix< double >	colCoord_

RowMatrix< double >	ppalAxes_

RowMatrix< double >	ppalComponents_

Detailed Description

The core class of a multivariate analysis.

In the constructor, the eigen values and vectors of the variance-covariance or correlation matrix are calculated. Eigen values and vectors are stored in the eigenValues_ and eigenVectors_ respectively. Furthermore, four matrices are calculated: the row and column coordinates as well as the principal axes and components.

The code of this class is deeply inspired from the R code of the as.dudi function available in the ade4 package.

Definition at line 57 of file DualityDiagram.h.

Constructor & Destructor Documentation

◆ DualityDiagram() [1/2]

bpp::DualityDiagram::DualityDiagram ( )

inline

Build an empty DualityDiagram object.

Definition at line 77 of file DualityDiagram.h.

Referenced by clone().

◆ DualityDiagram() [2/2]

DualityDiagram::DualityDiagram	(	const Matrix< double > &	matrix,
		const std::vector< double > &	rowWeights,
		const std::vector< double > &	colWeights,
		unsigned int	nbAxes,
		double	tol = `0.0000001`,
		bool	verbose = `true`
	)
throw	(	Exception
	)

Build a new DualityDiagram object.

Parameters

matrix	The input data to analyse.
rowWeights	A vector of values specifying the weights of rows.
colWeights	A vector of values specifying the weights of columns.
nbAxes	The number of kept axes during the analysis.
tol	Tolerance threshold for null eigenvalues (a value less than tol times the first one is considered as null)
verbose	Should warnings be dispayed.

Exceptions

Exception if an error occured.

Definition at line 50 of file DualityDiagram.cpp.

◆ ~DualityDiagram()

DualityDiagram::~DualityDiagram ( )

virtual

Definition at line 288 of file DualityDiagram.cpp.

Member Function Documentation

◆ check_()

void DualityDiagram::check_	(	const Matrix< double > &	matrix,
		const std::vector< double > &	rowWeights,
		const std::vector< double > &	colWeights,
		unsigned int	nbAxes
	)
throw	(	Exception
	)

private

Definition at line 70 of file DualityDiagram.cpp.

◆ clone()

DualityDiagram* bpp::DualityDiagram::clone ( ) const

inlinevirtual

Create a copy of this object and send a pointer to it.

Returns: A pointer toward the copy object.

Implements bpp::Clonable.

Reimplemented in bpp::PrincipalComponentAnalysis.

Definition at line 114 of file DualityDiagram.h.

References DualityDiagram().

◆ compute_()

void DualityDiagram::compute_	(	const Matrix< double > &	matrix,
		double	tol,
		bool	verbose
	)

private

Definition at line 114 of file DualityDiagram.cpp.

References bpp::ApplicationTools::displayWarning(), bpp::Matrix< Scalar >::getNumberOfColumns(), bpp::Matrix< Scalar >::getNumberOfRows(), bpp::EigenValue< Real >::getRealEigenValues(), bpp::EigenValue< Real >::getV(), bpp::MatrixTools::hadamardMult(), bpp::EigenValue< Real >::isSymmetric(), bpp::MatrixTools::mult(), bpp::RowMatrix< Scalar >::resize(), and bpp::MatrixTools::transpose().

◆ computeVariancePercentagePerAxis()

std::vector<double> bpp::DualityDiagram::computeVariancePercentagePerAxis	(		)
throw	(	Exception
	)

◆ getColCoordinates()

const RowMatrix<double>& bpp::DualityDiagram::getColCoordinates	(		)	const
throw	(	Exception
	)

inline

Definition at line 151 of file DualityDiagram.h.

References colCoord_.

◆ getColumnWeights()

const std::vector<double> bpp::DualityDiagram::getColumnWeights	(		)	const
throw	(	Exception
	)

inline

Definition at line 148 of file DualityDiagram.h.

References colWeights_.

◆ getEigenValues()

const std::vector<double>& bpp::DualityDiagram::getEigenValues	(		)	const
throw	(	Exception
	)

inline

Definition at line 149 of file DualityDiagram.h.

References eigenValues_.

◆ getNbOfKeptAxes()

size_t bpp::DualityDiagram::getNbOfKeptAxes	(		)	const
throw	(	Exception
	)

inline

Definition at line 146 of file DualityDiagram.h.

References nbAxes_.

◆ getPrincipalAxes()

const RowMatrix<double>& bpp::DualityDiagram::getPrincipalAxes	(		)	const
throw	(	Exception
	)

inline

Definition at line 152 of file DualityDiagram.h.

References ppalAxes_.

◆ getPrincipalComponents()

const RowMatrix<double>& bpp::DualityDiagram::getPrincipalComponents	(		)	const
throw	(	Exception
	)

inline

Definition at line 153 of file DualityDiagram.h.

References ppalComponents_.

◆ getRowCoordinates()

const RowMatrix<double>& bpp::DualityDiagram::getRowCoordinates	(		)	const
throw	(	Exception
	)

inline

Definition at line 150 of file DualityDiagram.h.

References rowCoord_.

◆ getRowWeights()

const std::vector<double> bpp::DualityDiagram::getRowWeights	(		)	const
throw	(	Exception
	)

inline

Definition at line 147 of file DualityDiagram.h.

References rowWeights_.

◆ setData()

void DualityDiagram::setData	(	const Matrix< double > &	matrix,
		const std::vector< double > &	rowWeights,
		const std::vector< double > &	colWeights,
		unsigned int	nbAxes,
		double	tol = `0.0000001`,
		bool	verbose = `true`
	)
throw	(	Exception
	)

Set the data and perform computations.

Parameters

matrix	The input data to analyse.
rowWeights	A vector of values specifying the weights of rows.
colWeights	A vector of values specifying the weights of columns.
nbAxes	The number of kept axes during the analysis.
tol	Tolerance threshold for null eigenvalues (a value less than tol times the first one is considered as null)
verbose	Should warnings be dispayed.

Exceptions

Exception if an error occured.

Definition at line 100 of file DualityDiagram.cpp.

Member Data Documentation

◆ colCoord_

RowMatrix<double> bpp::DualityDiagram::colCoord_

private

Definition at line 68 of file DualityDiagram.h.

Referenced by getColCoordinates().

◆ colWeights_

std::vector<double> bpp::DualityDiagram::colWeights_

private

Definition at line 63 of file DualityDiagram.h.

Referenced by getColumnWeights().

◆ eigenValues_

std::vector<double> bpp::DualityDiagram::eigenValues_

private

Definition at line 65 of file DualityDiagram.h.

Referenced by getEigenValues().

◆ eigenVectors_

RowMatrix<double> bpp::DualityDiagram::eigenVectors_

private

Definition at line 66 of file DualityDiagram.h.

◆ nbAxes_

size_t bpp::DualityDiagram::nbAxes_

private

Definition at line 64 of file DualityDiagram.h.

Referenced by getNbOfKeptAxes().

◆ ppalAxes_

RowMatrix<double> bpp::DualityDiagram::ppalAxes_

private

Definition at line 69 of file DualityDiagram.h.

Referenced by getPrincipalAxes().

◆ ppalComponents_

RowMatrix<double> bpp::DualityDiagram::ppalComponents_

private

Definition at line 70 of file DualityDiagram.h.

Referenced by getPrincipalComponents().

◆ rowCoord_

RowMatrix<double> bpp::DualityDiagram::rowCoord_

private

Definition at line 67 of file DualityDiagram.h.

Referenced by getRowCoordinates().

◆ rowWeights_

std::vector<double> bpp::DualityDiagram::rowWeights_

private

Definition at line 62 of file DualityDiagram.h.

Referenced by getRowWeights().

The documentation for this class was generated from the following files:

Bpp/Numeric/Stat/Mva/DualityDiagram.h
Bpp/Numeric/Stat/Mva/DualityDiagram.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DualityDiagram() [1/2]

◆ DualityDiagram() [2/2]

◆ ~DualityDiagram()

Member Function Documentation

◆ check_()

◆ clone()

◆ compute_()

◆ computeVariancePercentagePerAxis()

◆ getColCoordinates()

◆ getColumnWeights()

◆ getEigenValues()

◆ getNbOfKeptAxes()

◆ getPrincipalAxes()

◆ getPrincipalComponents()

◆ getRowCoordinates()

◆ getRowWeights()

◆ setData()

Member Data Documentation

◆ colCoord_

◆ colWeights_

◆ eigenValues_

◆ eigenVectors_

◆ nbAxes_

◆ ppalAxes_

◆ ppalComponents_

◆ rowCoord_

◆ rowWeights_