bpp::CorrespondenceAnalysis Class Reference

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 Attributes
double	n_

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 23 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 13 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 45 of file CorrespondenceAnalysis.h.

Member Function Documentation

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 47 of file CorrespondenceAnalysis.h.

References CorrespondenceAnalysis().

computeVariancePercentagePerAxis()

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

inherited

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

getColCoordinates()

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

inlineinherited

Definition at line 110 of file DualityDiagram.h.

References bpp::DualityDiagram::colCoord_.

getColumnWeights()

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

inlineinherited

Definition at line 107 of file DualityDiagram.h.

References bpp::DualityDiagram::colWeights_.

getEigenValues()

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

inlineinherited

Definition at line 108 of file DualityDiagram.h.

References bpp::DualityDiagram::eigenValues_.

getNbOfKeptAxes()

size_t bpp::DualityDiagram::getNbOfKeptAxes ( ) const

inlineinherited

Definition at line 105 of file DualityDiagram.h.

References bpp::DualityDiagram::nbAxes_.

getPrincipalAxes()

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

inlineinherited

Definition at line 111 of file DualityDiagram.h.

References bpp::DualityDiagram::ppalAxes_.

getPrincipalComponents()

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

inlineinherited

Definition at line 112 of file DualityDiagram.h.

References bpp::DualityDiagram::ppalComponents_.

getRowCoordinates()

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

inlineinherited

Definition at line 109 of file DualityDiagram.h.

References bpp::DualityDiagram::rowCoord_.

getRowWeights()

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

inlineinherited

Definition at line 106 of file DualityDiagram.h.

References bpp::DualityDiagram::rowWeights_.

getSumOfAllValues()

double bpp::CorrespondenceAnalysis::getSumOfAllValues ( ) const

inline

Definition at line 50 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.

Exceptions

Exception

if an error occured.

Definition at line 66 of file DualityDiagram.cpp.

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

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

Member Data Documentation

n_

double bpp::CorrespondenceAnalysis::n_

private

Definition at line 27 of file CorrespondenceAnalysis.h.

Referenced by CorrespondenceAnalysis(), and getSumOfAllValues().

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

• Bpp/Numeric/Stat/Mva/CorrespondenceAnalysis.h
• Bpp/Numeric/Stat/Mva/CorrespondenceAnalysis.cpp