This class allows to perform a principal component analysis. More...

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

Inheritance diagram for bpp::PrincipalComponentAnalysis:

Collaboration diagram for bpp::PrincipalComponentAnalysis:

Public Member Functions
	PrincipalComponentAnalysis (const Matrix< double > &data, unsigned int nbAxes, const std::vector< double > &rowW, const std::vector< double > &colW, bool centered=true, bool scaled=true, double tol=0.0000001, bool verbose=true)
	Build a new PrincipalComponentAnalysis object. More...

	PrincipalComponentAnalysis (const Matrix< double > &data, unsigned int nbAxes, bool centered=true, bool scaled=true, double tol=0.0000001, bool verbose=true)
	Build a new PrincipalComponentAnalysis object and specify default row and column weights. More...

virtual	~PrincipalComponentAnalysis ()

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

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

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

Static Public Member Functions
static void	center (Matrix< double > &matrix, const std::vector< double > &rowW)
	This function allows to center an input matrix from its column means. More...

static void	scale (Matrix< double > &matrix, const std::vector< double > &rowW)
	This function allows to center an input matrix from its column means. More...

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
std::vector< double >	columnMeans_

std::vector< double >	columnSd_

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 principal component analysis.

Two constructors are available. The first one allows the user to specify the row and column weights. The second one specify default weights: uniform weights unit weights are created for rows and columns respectively.

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

Definition at line 58 of file PrincipalComponentAnalysis.h.

Constructor & Destructor Documentation

◆ PrincipalComponentAnalysis() [1/2]

PrincipalComponentAnalysis::PrincipalComponentAnalysis	(	const Matrix< double > &	data,
		unsigned int	nbAxes,
		const std::vector< double > &	rowW,
		const std::vector< double > &	colW,
		bool	centered = `true`,
		bool	scaled = `true`,
		double	tol = `0.0000001`,
		bool	verbose = `true`
	)

Build a new PrincipalComponentAnalysis object.

Parameters

data	The input data (a RowMatrix) to analyse.
nbAxes	The number of kept axes during the analysis.
rowW	A vector of values specifying the weights of rows.
colW	A vector of values specifying the weights of columns.
centered	If true the input matrix is centered according to the column means.
scaled	If true the input matrix is normalized according to the standard deviations of columns.
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 51 of file PrincipalComponentAnalysis.cpp.

References center(), scale(), and bpp::DualityDiagram::setData().

Referenced by clone().

◆ PrincipalComponentAnalysis() [2/2]

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

Build a new PrincipalComponentAnalysis object and specify default row and column weights.

Parameters

data	The input data (a RowMatrix) to analyse.
nbAxes	The number of kept axes during the analysis.
centered	If true the input matrix is centered according to the column means.
scaled	If true the input matrix is normalized according to the standard deviations of columns.
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 83 of file PrincipalComponentAnalysis.cpp.

References center(), bpp::VectorTools::fill(), bpp::Matrix< Scalar >::getNumberOfColumns(), bpp::Matrix< Scalar >::getNumberOfRows(), scale(), and bpp::DualityDiagram::setData().

◆ ~PrincipalComponentAnalysis()

virtual bpp::PrincipalComponentAnalysis::~PrincipalComponentAnalysis ( )

inlinevirtual

Definition at line 108 of file PrincipalComponentAnalysis.h.

Member Function Documentation

◆ center()

void PrincipalComponentAnalysis::center	(	Matrix< double > &	matrix,
		const std::vector< double > &	rowW
	)

static

This function allows to center an input matrix from its column means.

Parameters

matrix	The input data (a Matrix) to center.
rowW	A vector with row weights.

Definition at line 121 of file PrincipalComponentAnalysis.cpp.

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

Referenced by PrincipalComponentAnalysis().

◆ 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()

PrincipalComponentAnalysis* bpp::PrincipalComponentAnalysis::clone ( ) const

inlinevirtual

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

Returns: A pointer toward the copy object.

Reimplemented from bpp::DualityDiagram.

Definition at line 110 of file PrincipalComponentAnalysis.h.

References PrincipalComponentAnalysis().

◆ 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_.

◆ getColumnMeans()

const std::vector<double>& bpp::PrincipalComponentAnalysis::getColumnMeans ( ) const

inline

Definition at line 130 of file PrincipalComponentAnalysis.h.

References columnMeans_.

◆ getColumnSd()

const std::vector<double>& bpp::PrincipalComponentAnalysis::getColumnSd ( ) const

inline

Definition at line 131 of file PrincipalComponentAnalysis.h.

References columnSd_.

◆ 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_.

◆ scale()

void PrincipalComponentAnalysis::scale	(	Matrix< double > &	matrix,
		const std::vector< double > &	rowW
	)

static

This function allows to center an input matrix from its column means.

Parameters

matrix	The input data (a Matrix) to center.
rowW	A vector with row weights.

Definition at line 152 of file PrincipalComponentAnalysis.cpp.

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

Referenced by PrincipalComponentAnalysis().

◆ 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.

Exceptions

Exception if an error occured.

Definition at line 101 of file DualityDiagram.cpp.

References bpp::DualityDiagram::check_(), bpp::DualityDiagram::colWeights_, bpp::DualityDiagram::compute_(), bpp::DualityDiagram::nbAxes_, and bpp::DualityDiagram::rowWeights_.

Referenced by bpp::CorrespondenceAnalysis::CorrespondenceAnalysis(), and PrincipalComponentAnalysis().

Member Data Documentation

◆ colCoord_

RowMatrix<double> bpp::DualityDiagram::colCoord_

privateinherited

Definition at line 68 of file DualityDiagram.h.

Referenced by bpp::DualityDiagram::compute_(), and bpp::DualityDiagram::getColCoordinates().

◆ columnMeans_

std::vector<double> bpp::PrincipalComponentAnalysis::columnMeans_

private

Definition at line 62 of file PrincipalComponentAnalysis.h.

Referenced by getColumnMeans().

◆ columnSd_

std::vector<double> bpp::PrincipalComponentAnalysis::columnSd_

private

Definition at line 63 of file PrincipalComponentAnalysis.h.

Referenced by getColumnSd().

◆ colWeights_

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

privateinherited

Definition at line 63 of file DualityDiagram.h.

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

◆ eigenValues_

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

privateinherited

Definition at line 65 of file DualityDiagram.h.

Referenced by bpp::DualityDiagram::compute_(), and bpp::DualityDiagram::getEigenValues().

◆ eigenVectors_

RowMatrix<double> bpp::DualityDiagram::eigenVectors_

privateinherited

Definition at line 66 of file DualityDiagram.h.

Referenced by bpp::DualityDiagram::compute_().

◆ nbAxes_

size_t bpp::DualityDiagram::nbAxes_

privateinherited

Definition at line 64 of file DualityDiagram.h.

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

◆ ppalAxes_

RowMatrix<double> bpp::DualityDiagram::ppalAxes_

privateinherited

Definition at line 69 of file DualityDiagram.h.

Referenced by bpp::DualityDiagram::compute_(), and bpp::DualityDiagram::getPrincipalAxes().

◆ ppalComponents_

RowMatrix<double> bpp::DualityDiagram::ppalComponents_

privateinherited

Definition at line 70 of file DualityDiagram.h.

Referenced by bpp::DualityDiagram::compute_(), and bpp::DualityDiagram::getPrincipalComponents().

◆ rowCoord_

RowMatrix<double> bpp::DualityDiagram::rowCoord_

privateinherited

Definition at line 67 of file DualityDiagram.h.

Referenced by bpp::DualityDiagram::compute_(), and bpp::DualityDiagram::getRowCoordinates().

◆ rowWeights_

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

privateinherited

Definition at line 62 of file DualityDiagram.h.

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

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

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

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PrincipalComponentAnalysis() [1/2]

◆ PrincipalComponentAnalysis() [2/2]

◆ ~PrincipalComponentAnalysis()

Member Function Documentation

◆ center()

◆ check_()

◆ clone()

◆ compute_()

◆ computeVariancePercentagePerAxis()

◆ getColCoordinates()

◆ getColumnMeans()

◆ getColumnSd()

◆ getColumnWeights()

◆ getEigenValues()

◆ getNbOfKeptAxes()

◆ getPrincipalAxes()

◆ getPrincipalComponents()

◆ getRowCoordinates()

◆ getRowWeights()

◆ scale()

◆ setData()

Member Data Documentation

◆ colCoord_

◆ columnMeans_

◆ columnSd_

◆ colWeights_

◆ eigenValues_

◆ eigenVectors_

◆ nbAxes_

◆ ppalAxes_

◆ ppalComponents_

◆ rowCoord_

◆ rowWeights_