BALL::QSAR::PCRModel Class Reference

#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_
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
RegressionValidation *	validation
const QSARData *	data
Validation *	model_val
void	calculateOffsets ()
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

PCRModel()

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

~PCRModel()

BALL::QSAR::PCRModel::~PCRModel

(

)

Member Function Documentation

calculateEigenvectors()

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

getParameters()

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

virtual

Reimplemented from BALL::QSAR::Model.

setFracVar()

void BALL::QSAR::PCRModel::setFracVar

(

double

frac_var

)

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

setParameters()

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

virtual

sets the model parameters according to the given values.

Reimplemented from BALL::QSAR::Model.

train()

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

frac_var_

double BALL::QSAR::PCRModel::frac_var_

protected

fraction of the variance that is to be explained

Definition at line 68 of file pcrModel.h.