#include <BALL/QSAR/regressionValidation.h>

Inheritance diagram for BALL::QSAR::RegressionValidation:

Public Member Functions
Constructors and Destructors
	RegressionValidation (RegressionModel *m)

	~RegressionValidation ()

Public Member Functions inherited from BALL::QSAR::Validation
	Validation (Model *m)

virtual	~Validation ()

const Eigen::MatrixXd &	getYRandResults () const

int	getStat () const

Accessors
void	crossValidation (int k, bool restore=true)

void	crossValidation (int k, MatrixVector *results, bool restore=true)

void	bootstrap (int k, bool restore=1)

void	bootstrap (int k, MatrixVector *results, bool restore=true)

void	bootstrap1 (int k, MatrixVector *results, bool restore=true)

const Eigen::MatrixXd &	yRandomizationTest (int runs, int k)

double	getQ2 ()

double	getR2 ()

double	getFregr ()

double	getFcv ()

double	getCVRes ()

double	getFitRes ()

double	getMaxError ()

void	setCVRes (double d)

void	setQ2 (double d)

void	testInputData (bool transform=0)

void	selectStat (int s)

void	calculateCoefficientStdErrors (int k, bool b=1)

const Eigen::MatrixXd *	getCoefficientStdErrors ()

void	setCoefficientStdErrors (const Eigen::MatrixXd *stddev)

void	saveToFile (string filename) const

void	saveToFile (string filename, const double &r2, const double &q2, const Eigen::MatrixXd &coefficient_stddev, const Eigen::MatrixXd &yRand_results) const

void	readFromFile (string filename)

Additional Inherited Members
Protected Member Functions inherited from BALL::QSAR::Validation
void	setTrainingLine (int train_line, int current_line)

void	setTestLine (int test_line, int current_line, bool back_transform=0)

void	yRand ()

Protected Attributes inherited from BALL::QSAR::Validation
vector< vector< double > >	test_substances_

Eigen::MatrixXd	test_Y_

vector< string >	substances_names_

Model *	model_

int	validation_statistic_

Eigen::MatrixXd	yRand_results_

Detailed Description

class for validation of QSAR regression models

Definition at line 23 of file regressionValidation.h.

Constructor & Destructor Documentation

BALL::QSAR::RegressionValidation::RegressionValidation ( RegressionModel * m )

constructor

Parameters

m	pointer to the regression model, which the object of this class should test

BALL::QSAR::RegressionValidation::~RegressionValidation ( )

Member Function Documentation

void BALL::QSAR::RegressionValidation::bootstrap	(	int	k,
		bool	restore = `1`
	)

virtual

starts bootstrapping with k samples

Parameters

k	no of bootstrap samples
restore	if restore==1, Model.descriptor_matrix and RegressionModel.training_result is restored after bootstrapping

Implements BALL::QSAR::Validation.

void BALL::QSAR::RegressionValidation::bootstrap	(	int	k,
		MatrixVector *	results,
		bool	restore = `true`
	)

starts bootstrapping with k samples

Parameters

k	no of bootstrap samples
restore	if restore==1, Model.descriptor_matrix and RegressionModel.training_result is restored after bootstrapping
results	pointer to vector that should take all matrices RegressionModel.training_result produced during this bootstrapping

void BALL::QSAR::RegressionValidation::bootstrap1	(	int	k,
		MatrixVector *	results,
		bool	restore = `true`
	)

void BALL::QSAR::RegressionValidation::calculateCoefficientStdErrors	(	int	k,
		bool	b = `1`
	)

calculates standart deviations for all predicted coefficients and saves them to coefficient_stddev_

Parameters

b	if b==1, bootstrapping is used; else: cross-validation
k	number of bootstrap samples resp. cross-validation steps

void BALL::QSAR::RegressionValidation::crossValidation	(	int	k,
		bool	restore = `true`
	)

virtual

starts k-fold cross validation

Parameters

k	no of cross validation folds
restore	if restore==1, Model.descriptor_matrix and RegressionModel.training_result is restored after cross validation

Implements BALL::QSAR::Validation.

void BALL::QSAR::RegressionValidation::crossValidation	(	int	k,
		MatrixVector *	results,
		bool	restore = `true`
	)

starts k-fold cross validation

Parameters

k	no of cross validation folds
restore	if restore==1, Model.descriptor_matrix and RegressionModel.training_result is restored after cross validation
results	pointer to vector that should take all matrices RegressionModel.training_result produced during this cross validation run

const Eigen::MatrixXd* BALL::QSAR::RegressionValidation::getCoefficientStdErrors ( )

returns a const pointer to the matrix containing the standart deviations of all predicted coefficients

double BALL::QSAR::RegressionValidation::getCVRes ( )

virtual

fetches the result of cross-validation

Implements BALL::QSAR::Validation.

double BALL::QSAR::RegressionValidation::getFcv ( )

get the F-value as calculated by cross validation.
If crossValidation() has not been run yet, -1 is returned

double BALL::QSAR::RegressionValidation::getFitRes ( )

virtual

fetches the quality of fit to the input data, as calculated by testInputData()

Implements BALL::QSAR::Validation.

double BALL::QSAR::RegressionValidation::getFregr ( )

get the F-value as calculated by testInputData().
If testInputData() has not been run yet, -1 is returned

double BALL::QSAR::RegressionValidation::getMaxError ( )

returns the maximal error of the prediction

double BALL::QSAR::RegressionValidation::getQ2 ( )

get the Q^2 value.
If no cross-validation has been done yet, -1 is returned

double BALL::QSAR::RegressionValidation::getR2 ( )

get the R^2 value.
If testInputData() has not been run yet, -1 is returned

void BALL::QSAR::RegressionValidation::readFromFile ( string filename )

virtual

restore validation-results from a file

Implements BALL::QSAR::Validation.

void BALL::QSAR::RegressionValidation::saveToFile ( string filename ) const

virtual

save the result of the applied validation methods to a file

Implements BALL::QSAR::Validation.

void BALL::QSAR::RegressionValidation::saveToFile	(	string	filename,
		const double &	r2,
		const double &	q2,
		const Eigen::MatrixXd &	coefficient_stddev,
		const Eigen::MatrixXd &	yRand_results
	)		const

void BALL::QSAR::RegressionValidation::selectStat ( int s )

virtual

select the desired statistic to be used for validating the models

Parameters

s	if (s==1) R^2 and Q^2 are used if(s==2) F_regr and F_cv are used.

Implements BALL::QSAR::Validation.

void BALL::QSAR::RegressionValidation::setCoefficientStdErrors ( const Eigen::MatrixXd * stddev )

void BALL::QSAR::RegressionValidation::setCVRes ( double d )

virtual

set the result of cross-validation to the given value

Implements BALL::QSAR::Validation.

void BALL::QSAR::RegressionValidation::setQ2 ( double d )

set the Q^2 value

void BALL::QSAR::RegressionValidation::testInputData ( bool transform = 0 )

virtual

Fetches input data from QSARData and tests the current (unchanged) model with all these new substances (without cross-validation!).

Parameters

transform if transform==1, the test data is transformed in the same way that the training data was transformed before predicting activities.
If training and test substances are taken from the same input file, set transform to 0

Implements BALL::QSAR::Validation.

const Eigen::MatrixXd& BALL::QSAR::RegressionValidation::yRandomizationTest	(	int	runs,
		int	k
	)

virtual

Y randomization test
Randomizes all columns of model.Y, trains the model, runs crossValidation and testInputData and saves the resulting R2 and Q2 value to a matrix with 2 columns; the R2 values makeing up the first colum, the Q2 value the second.

Parameters

runs	this is repeated as often as specified by 'runs'

Implements BALL::QSAR::Validation.

Public Member Functions

Accessors

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation