This class allows to perform a correspondence analysis. More...

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

Inheritance diagram for bpp::CorrespondenceAnalysis:

Collaboration diagram for bpp::CorrespondenceAnalysis:

Public Member Functions
	CorrespondenceAnalysis (const Matrix< double > &data, unsigned int nbAxes, double tol=0.0000001, bool verbose=true)
	Build a new CorrespondenceAnalysis object. More...

virtual	~CorrespondenceAnalysis ()

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

double	getSumOfAllValues () const

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)
	Set the data and perform computations. More...

std::vector< double >	computeVariancePercentagePerAxis ()

size_t	getNbOfKeptAxes () const

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

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

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

const RowMatrix< double > &	getRowCoordinates () const

const RowMatrix< double > &	getColCoordinates () const

const RowMatrix< double > &	getPrincipalAxes () const

const RowMatrix< double > &	getPrincipalComponents () const

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

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

Private Attributes
double	n_

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

This class allows to perform a correspondence analysis.

All values in the input table have to be non-negative. The DualityDiagram class, core class of a multivariate analysis, is called internally.

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

Definition at line 59 of file CorrespondenceAnalysis.h.

Constructor & Destructor Documentation

◆ CorrespondenceAnalysis()

CorrespondenceAnalysis::CorrespondenceAnalysis	(	const Matrix< double > &	data,
		unsigned int	nbAxes,
		double	tol = `0.0000001`,
		bool	verbose = `true`
	)

Build a new CorrespondenceAnalysis object.

Parameters

data	The input data (a RowMatrix) to analyse.
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 CorrespondenceAnalysis.cpp.

References bpp::Matrix< Scalar >::getNumberOfColumns(), bpp::Matrix< Scalar >::getNumberOfRows(), bpp::MatrixTools::hadamardMult(), n_, bpp::MatrixTools::scale(), and bpp::DualityDiagram::setData().

Referenced by clone().

◆ ~CorrespondenceAnalysis()

virtual bpp::CorrespondenceAnalysis::~CorrespondenceAnalysis ( )

inlinevirtual

Definition at line 81 of file CorrespondenceAnalysis.h.

Member Function Documentation

◆ check_()

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

privateinherited

Definition at line 71 of file DualityDiagram.cpp.

References bpp::Matrix< Scalar >::getNumberOfColumns(), and bpp::Matrix< Scalar >::getNumberOfRows().

Referenced by bpp::DualityDiagram::DualityDiagram(), and bpp::DualityDiagram::setData().

◆ clone()

CorrespondenceAnalysis* bpp::CorrespondenceAnalysis::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.

Definition at line 83 of file CorrespondenceAnalysis.h.

References CorrespondenceAnalysis().

◆ compute_()

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

privateinherited

Definition at line 115 of file DualityDiagram.cpp.

References bpp::DualityDiagram::colCoord_, bpp::DualityDiagram::colWeights_, bpp::ApplicationTools::displayWarning(), bpp::DualityDiagram::eigenValues_, bpp::DualityDiagram::eigenVectors_, bpp::RowMatrix< Scalar >::getNumberOfColumns(), bpp::Matrix< Scalar >::getNumberOfColumns(), bpp::RowMatrix< Scalar >::getNumberOfRows(), bpp::Matrix< Scalar >::getNumberOfRows(), bpp::EigenValue< Real >::getRealEigenValues(), bpp::EigenValue< Real >::getV(), bpp::MatrixTools::hadamardMult(), bpp::EigenValue< Real >::isSymmetric(), bpp::MatrixTools::mult(), bpp::DualityDiagram::nbAxes_, bpp::DualityDiagram::ppalAxes_, bpp::DualityDiagram::ppalComponents_, bpp::RowMatrix< Scalar >::resize(), bpp::DualityDiagram::rowCoord_, bpp::DualityDiagram::rowWeights_, and bpp::MatrixTools::transpose().

Referenced by bpp::DualityDiagram::DualityDiagram(), and bpp::DualityDiagram::setData().

◆ computeVariancePercentagePerAxis()

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

inherited

◆ getColCoordinates()

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

inlineinherited

Definition at line 146 of file DualityDiagram.h.

References bpp::DualityDiagram::colCoord_.

◆ getColumnWeights()

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

inlineinherited

Definition at line 143 of file DualityDiagram.h.

References bpp::DualityDiagram::colWeights_.

◆ getEigenValues()

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

inlineinherited

Definition at line 144 of file DualityDiagram.h.

References bpp::DualityDiagram::eigenValues_.

◆ getNbOfKeptAxes()

size_t bpp::DualityDiagram::getNbOfKeptAxes ( ) const

inlineinherited

Definition at line 141 of file DualityDiagram.h.

References bpp::DualityDiagram::nbAxes_.

◆ getPrincipalAxes()

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

inlineinherited

Definition at line 147 of file DualityDiagram.h.

References bpp::DualityDiagram::ppalAxes_.

◆ getPrincipalComponents()

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

inlineinherited

Definition at line 148 of file DualityDiagram.h.

References bpp::DualityDiagram::ppalComponents_.

◆ getRowCoordinates()

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

inlineinherited

Definition at line 145 of file DualityDiagram.h.

References bpp::DualityDiagram::rowCoord_.

◆ getRowWeights()

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

inlineinherited

Definition at line 142 of file DualityDiagram.h.

References bpp::DualityDiagram::rowWeights_.

◆ getSumOfAllValues()

double bpp::CorrespondenceAnalysis::getSumOfAllValues ( ) const

inline

Definition at line 86 of file CorrespondenceAnalysis.h.

References n_.

◆ 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`
	)

inherited

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.