#include <BALL/QSAR/pcrModel.h>

Inheritance diagram for BALL::QSAR::PCRModel:

Public Member Functions
Constructors and Destructors
	PCRModel (const QSARData &q, double frac_var=0.99)

	~PCRModel ()

Public Member Functions inherited from BALL::QSAR::LinearModel
	LinearModel (const QSARData &q)

	~LinearModel ()

virtual void	operator= (const LinearModel &m)

virtual Eigen::VectorXd	predict (const vector< double > &substance, bool transform=1)

Public Member Functions inherited from BALL::QSAR::RegressionModel
	RegressionModel (const QSARData &q)

	~RegressionModel ()

virtual EIGEN_MAKE_ALIGNED_OPERATOR_NEW void	operator= (const RegressionModel &m)

const Eigen::MatrixXd *	getTrainingResult () const

virtual void	saveToFile (string filename)

virtual void	readFromFile (string filename)

void	show ()

Public Member Functions inherited from BALL::QSAR::Model
	Model (const QSARData &q)

virtual	~Model ()

virtual void	operator= (const Model &m)

void	copyData (const Model &m)

void	copyDescriptorIDs (const Model &m)

void	readTrainingData ()

void	deleteDescriptorIDs ()

virtual bool	optimizeParameters (int, int)

bool	optimizeParameters (int k)

virtual double	calculateStdErr ()

std::multiset< unsigned int > *	getDescriptorIDs ()

void	setDataSource (const QSARData *q)

const Eigen::MatrixXd *	getDescriptorMatrix ()

const vector< string > *	getSubstanceNames ()

const vector< string > *	getDescriptorNames ()

const Eigen::MatrixXd	getDescriptorTransformations ()

const Eigen::MatrixXd	getYTransformations ()

const Eigen::MatrixXd *	getY ()

void	setDescriptorIDs (const std::multiset< unsigned int > &sl)

const string *	getType ()

void	getUnnormalizedFeatureValue (int compound, int feature, double &return_value)

void	getUnnormalizedResponseValue (int compound, int response, double &return_value)

Public Member Functions inherited from BALL::QSAR::LatentVariableModel
	LatentVariableModel ()

const Eigen::MatrixXd *	getLatentVariables ()

const Eigen::MatrixXd *	getWeights ()

const Eigen::MatrixXd *	getLoadings ()

Protected Attributes
Attributes
double	frac_var_

Protected Attributes inherited from BALL::QSAR::RegressionModel
Eigen::MatrixXd	training_result_

Eigen::RowVectorXd	offsets_

Protected Attributes inherited from BALL::QSAR::Model
int	default_no_opt_steps_

Eigen::MatrixXd	descriptor_matrix_

vector< string >	substance_names_

vector< string >	descriptor_names_

Eigen::MatrixXd	descriptor_transformations_

Eigen::MatrixXd	y_transformations_

Eigen::MatrixXd	Y_

String	type_

std::multiset< unsigned int >	descriptor_IDs_

Protected Attributes inherited from BALL::QSAR::LatentVariableModel
Eigen::MatrixXd	latent_variables_

Eigen::MatrixXd	loadings_

Eigen::MatrixXd	weights_

Accessors
void	train ()

void	setFracVar (double frac_var)

void	setParameters (vector< double > &v)

vector< double >	getParameters () const

static void	calculateEigenvectors (const Eigen::MatrixXd &data, double frac_var, Eigen::MatrixXd &output)

Additional Inherited Members
Public Attributes inherited from BALL::QSAR::RegressionModel
RegressionValidation *	validation

Public Attributes inherited from BALL::QSAR::Model
const QSARData *	data

Validation *	model_val

Protected Member Functions inherited from BALL::QSAR::LinearModel
void	calculateOffsets ()

Protected Member Functions inherited from BALL::QSAR::RegressionModel
void	readDescriptorInformationFromFile (std::ifstream &in, int no_descriptors, bool transformation, int no_coefficients)

void	saveDescriptorInformationToFile (std::ofstream &out)

Protected Member Functions inherited from BALL::QSAR::Model
void	readMatrix (Eigen::MatrixXd &mat, std::ifstream &in, unsigned int lines, unsigned int col)

void	readVector (Eigen::RowVectorXd &vec, std::ifstream &in, unsigned int no_cells, bool column_vector)

void	readModelParametersFromFile (std::ifstream &in)

void	saveModelParametersToFile (std::ofstream &out)

virtual void	readDescriptorInformationFromFile (std::ifstream &in, int no_descriptors, bool transformation)

void	readResponseTransformationFromFile (std::ifstream &in, int no_y)

void	saveResponseTransformationToFile (std::ofstream &out)

Eigen::VectorXd	getSubstanceVector (const vector< double > &substance, bool transform)

Eigen::VectorXd	getSubstanceVector (const Eigen::VectorXd &substance, bool transform)

void	backTransformPrediction (Eigen::VectorXd &pred)

void	addLambda (Eigen::MatrixXd &matrix, double &lambda)

void	readDescriptorInformation ()

Detailed Description

Definition at line 26 of file pcrModel.h.

Constructor & Destructor Documentation

BALL::QSAR::PCRModel::PCRModel	(	const QSARData &	q,
		double	frac_var = `0.99`
	)

constructur

Parameters

q	QSAR-wrapper object, from which the data for this model should be taken
frac_var	the part of the variance that is to be explained by the latent variables; as many latent variables as necessary to achieve this are created

BALL::QSAR::PCRModel::~PCRModel ( )

Member Function Documentation

static void BALL::QSAR::PCRModel::calculateEigenvectors	(	const Eigen::MatrixXd &	data,
		double	frac_var,
		Eigen::MatrixXd &	output
	)

static

calculates the first eigenvectors of the given matrix 'data' and saves them as columns of matrix 'output'

Parameters

frac_var the fraction of the variance that is to the covered the selected eigenvectors

vector<double> BALL::QSAR::PCRModel::getParameters ( ) const

virtual

Reimplemented from BALL::QSAR::Model.

void BALL::QSAR::PCRModel::setFracVar ( double frac_var )

set the fraction of the variance that should be explained by the latente variables.

void BALL::QSAR::PCRModel::setParameters ( vector< double > & )

virtual

sets the model parameters according to the given values.

Reimplemented from BALL::QSAR::Model.

void BALL::QSAR::PCRModel::train ( )

virtual

Starts principal component regression with the current data and saves the resulting linear combination of descriptors to training_result.

Implements BALL::QSAR::Model.

Member Data Documentation

double BALL::QSAR::PCRModel::frac_var_

protected

fraction of the variance that is to be explained

Definition at line 68 of file pcrModel.h.

Public Member Functions

Protected Attributes

Accessors

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation