Regression with independent blocks of traits. More...

#include <MuGen.h>

Inheritance diagram for BetaBlk:

Collaboration diagram for BetaBlk:

Public Member Functions
	BetaBlk ()
	Default constructor.

	BetaBlk (const Grp &dat, const string &predFlName, const size_t &Npred, const string &blkIndFileNam, const int &nThr)
	Basic constructor. More...

	BetaBlk (const Grp &dat, const string &predFlName, const size_t &Npred, const string &outFlNam, const string &blkIndFileNam, const int &nThr)
	Constructor with output file name. More...

	BetaBlk (const Grp &dat, const string &predFlName, const size_t &Npred, RanIndex &up, const string &blkIndFileNam, const int &nThr)
	Constructor with a prior index. More...

	BetaBlk (const Grp &dat, const string &predFlName, const size_t &Npred, RanIndex &up, const string &outFlNam, const string &blkIndFileNam, const int &nThr)
	Constructor with a prior index and output file. More...

	BetaBlk (const Grp &dat, const string &predFlName, const size_t &Npred, const double &absLab, const string &blkIndFileNam, const int &nThr)
	Constructor with missing predictor data. More...

	BetaBlk (const Grp &dat, const string &predFlName, const size_t &Npred, const double &absLab, const string &outFlNam, const string &blkIndFileNam, const int &nThr)
	Constructor with missing predictor values and output file name. More...

	BetaBlk (const Grp &dat, const string &predFlName, const size_t &Npred, const double &absLab, RanIndex &up, const string &blkIndFileNam, const int &nThr)
	Constructor with a prior index and missing predictor data. More...

	BetaBlk (const Grp &dat, const string &predFlName, const size_t &Npred, const double &absLab, RanIndex &up, const string &outFlNam, const string &blkIndFileNam, const int &nThr)
	Constructor with a prior index, missing predictor data, and output file. More...

	~BetaBlk ()
	Destructor.

Public Member Functions inherited from BetaGrpFt
	BetaGrpFt ()
	Default constructor.

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const int &nThr)
	Simple constructor. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, RanIndex &up, const int &nThr)
	Simple constructor with a prior index. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, RanIndex &low, RanIndex &up, const int &nThr)
	Simple constructor with a prior index and replication. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const string &outFlNam, const int &nThr)
	Simple constructor with output file name. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, RanIndex &up, const string &outFlNam, const int &nThr)
	Simple constructor with a prior index and output file name. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, RanIndex &low, RanIndex &up, const string &outFlNam, const int &nThr)
	Simple constructor with a prior index, replication and output file name. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const double &absLab, const int &nThr)
	Missing data constructor. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const double &absLab, RanIndex &up, const int &nThr)
	Missing data constructor with a prior index. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const double &absLab, RanIndex &low, RanIndex &up, const int &nThr)
	Missing data constructor with a prior index and replication. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const double &absLab, const string &outFlNam, const int &nThr)
	Missing data constructor with output file name. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const double &absLab, RanIndex &up, const string &outFlNam, const int &nThr)
	Missing data constructor with a prior index and output file name. More...

	BetaGrpFt (const Grp &rsp, const string &predFlNam, const size_t &Npred, const double &absLab, RanIndex &low, RanIndex &up, const string &outFlNam, const int &nThr)
	Missing data constructor with a prior index, replication and output file name. More...

	BetaGrpFt (const Grp &rsp, const SigmaI &SigI, const string &predFlNam, const size_t &Npred, const double &Nmul, const double &rSqMax, RanIndex &up, const string &outFlNam, const int &nThr)
	Selection constructor. More...

	BetaGrpFt (const Grp &rsp, const SigmaI &SigI, const string &predFlNam, const size_t &Npred, const double &Nmul, const double &rSqMax, RanIndex &low, RanIndex &up, const string &outFlNam, const int &nThr)
	Selection constructor with replication. More...

	BetaGrpFt (const Grp &rsp, const SigmaI &SigI, const string &predFlNam, const size_t &Npred, const double &Nmul, const double &rSqMax, const double &absLab, RanIndex &up, const string &outFlNam, const int &nThr)
	Selection constructor with missing predictor data. More...

	BetaGrpFt (const Grp &rsp, const SigmaI &SigI, const string &predFlNam, const size_t &Npred, const double &Nmul, const double &rSqMax, const double &absLab, RanIndex &low, RanIndex &up, const string &outFlNam, const int &nThr)
	Selection constructor with missing predictor data and replication. More...

virtual	~BetaGrpFt ()
	Destructor.

	BetaGrpFt (const BetaGrpFt &mG)
	Copy constructor. More...

BetaGrpFt &	operator= (const BetaGrpFt &mG)
	Assignment operator. More...

virtual const gsl_matrix *	fMat () const
	Access to the fitted value matrix. More...

void	save (const SigmaI &SigI)
	Store samples. More...

void	dump ()
	Dump to a file. More...

double	lnOddsRat (const Grp &y, const SigmaI &SigI, const size_t i) const
	Log-odds ratio. More...

void	update (const Grp &dat, const SigmaI &SigIm)
	Gaussian likelihood, improper prior. More...

void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm)
	Student- \(t\) likelihood, improper prior. More...

virtual void	update (const Grp &dat, const SigmaI &SigIm, const SigmaI &SigIp)
	Gaussian likelihood, 0-mean Gaussian prior. More...

virtual void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm, const SigmaI &SigIp)
	Student- \(t\) likelihood, 0-mean Gaussian prior. More...

virtual void	update (const Grp &dat, const SigmaI &SigIm, const Qgrp &qPr, const SigmaI &SigIp)
	Gaussian likelihood, 0-mean Student- \(t\) prior. More...

virtual void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm, const Qgrp &qPr, const SigmaI &SigIp)
	Student- \(t\) likelihood, 0-mean Student- \(t\) prior. More...

virtual void	update (const Grp &dat, const SigmaI &SigIm, const Grp &muPr, const SigmaI &SigIp)
	Gaussian likelihood, non-zero mean Gaussian prior. More...

virtual void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm, const Grp &muPr, const SigmaI &SigIp)
	Student- \(t\) likelihood, non-zero mean Gaussian prior. More...

virtual void	update (const Grp &dat, const SigmaI &SigIm, const Grp &muPr, const Qgrp &qPr, const SigmaI &SigIp)
	Gaussian likelihood, non-zero mean Student- \(t\) prior. More...

virtual void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm, const Grp &muPr, const Qgrp &qPr, const SigmaI &SigIp)
	Student- \(t\) likelihood, non-zero mean Student- \(t\) prior. More...

Public Member Functions inherited from Grp
virtual	~Grp ()
	Destructor.

virtual void	save ()
	Save to pre-specified file. More...

virtual void	save (const string &outFlNam)
	Save to file. More...

virtual void	save (const string &outMuFlNam, const string &outSigFlNam, const SigmaI &SigI)
	Joint save. More...

virtual void	save (const Grp &y, const SigmaI &SigI)
	Save with data and inverse-covariance. More...

void	mhlSave (const string &outFlNam, const SigmaI SigI)
	Save Mahalanobis distance. More...

const vector< MVnorm * > &	dataVec () const
	Get vector of row pointers. More...

virtual const gsl_matrix *	dMat () const
	Access the value matrix. More...

const size_t	Ndata () const
	Get number of rows. More...

const size_t	phenD () const
	Get number of traits. More...

const MVnorm *	operator[] (const size_t i) const
	Subscript operator. More...

MVnorm *	operator[] (const size_t i)
	Subscript operator. More...

virtual MuGrp	mean (RanIndex &grp)
	Group mean. More...

virtual const MuGrp	mean (RanIndex &grp) const
	Group mean. More...

virtual MuGrp	mean (RanIndex &grp, const Qgrp &q)
	Group weighted mean. More...

virtual const MuGrp	mean (RanIndex &grp, const Qgrp &q) const
	Group weighted mean. More...

void	center ()
	Center the value matrix. More...

Protected Member Functions
void	_updateFitted ()
	Update fitted values.

Protected Member Functions inherited from BetaGrpFt
void	_rankPred (const gsl_matrix y, const SigmaI &SigI, gsl_vector XtX, gsl_permutation *prm)
	Rank predictors. More...

void	_rankPred (const gsl_matrix y, const SigmaI &SigI, const double &absLab, gsl_vector XtX, gsl_permutation *prm)
	Rank predictors with missing data. More...

void	_ldToss (const gsl_vector var, const gsl_permutation prm, const double &rSqMax, const size_t &Npck, vector< vector< size_t > > &idx, vector< vector< size_t > > &rLd, gsl_matrix *Xpck)
	Testing candidates for correlation. More...

virtual double	_MGkernel (const Grp &dat, const SigmaI &SigI) const
	Gaussian kernel. More...

virtual double	_MGkernel (const Grp &dat, const SigmaI &SigI, const size_t &prInd) const
	Gaussian kernel dropping one predictor. More...

Protected Member Functions inherited from Grp
	Grp ()

Protected Attributes
vector< size_t >	_blkStart
	Block start indexes. More...

vector< gsl_matrix_view >	_eachX
	Predictor submatrices. More...

vector< gsl_matrix_view >	_eachB
	Regression coefficient submatrices. More...

Protected Attributes inherited from BetaGrpFt
vector< vector< double > >	_fittedEach
	Partial fitted value matrices. More...

gsl_matrix *	_fittedAll
	Matrix of fitted values. More...

gsl_matrix *	_valueSum
	Sample storage matrix. More...

gsl_matrix *	_Xmat
	Predictor matrix. More...

int	_nThr
	Number of threads.

double	_numSaves
	Number of saves. More...

Protected Attributes inherited from Grp
vector< MVnorm * >	_theta
	Vector of pointers to value rows. More...

gsl_matrix *	_valueMat
	Value matrix. More...

RanIndex *	_lowLevel
	Lower level index. More...

RanIndex *	_upLevel
	Upper level index. More...

vector< gsl_rng * >	_rV
	Vector of PNG pointers. More...

string	_outFlNam
	Name of the output file.

Detailed Description

Regression with independent blocks of traits.

Blocks of inter-correlated traits with correlations among blocks set to exactly zero. These models arise, for example, when traits measured in different environments are modeled together as different traits. The traits belonging to the same block have to be in adjacent columns. The number of predictors per block must be the same (future devolpment will drop this requirement), and the predictor columns corresponding to the same trait block have to be adjacent in the _Xmat matrix.

Constructor & Destructor Documentation

◆ BetaBlk() [1/8]

BetaBlk::BetaBlk	(	const Grp &	dat,
		const string &	predFlName,
		const size_t &	Npred,
		const string &	blkIndFileNam,
		const int &	nThr
	)

Basic constructor.

The total number of predictors (columns in Xmat) is the provided number of predictors times the number of blocks. The file that has the block start indexes should be a white-space delimited text file. The file that has the lower level index information should have a matrix of _int with the number of rows the same as the number of rows in the data, and the number of columns equal to the number of blocks.

Parameters

[in]	Grp&	data for initialization
[in]	string&	name of the predictor file
[in]	size_t&	number of predictors per block
[in]	string&	name of the file with the block indexes
[in]	int&	number of threads

◆ BetaBlk() [2/8]

BetaBlk::BetaBlk	(	const Grp &	dat,
		const string &	predFlName,
		const size_t &	Npred,
		const string &	outFlNam,
		const string &	blkIndFileNam,
		const int &	nThr
	)

Constructor with output file name.

The total number of predictors (columns in Xmat) is the provided number of predictors times the number of blocks. The file that has the block start indexes should be a white-space delimited text file. The file that has the lower level index information should have a matrix of _int with the number of rows the same as the number of rows in the data, and the number of columns equal to the number of blocks.

Parameters

[in]	Grp&	data for initialization
[in]	string&	name of the predictor file
[in]	size_t&	number of predictors per block
[in]	string&	output file name
[in]	string&	name of the file with the block indexes
[in]	int&	number of threads

◆ BetaBlk() [3/8]

BetaBlk::BetaBlk	(	const Grp &	dat,
		const string &	predFlName,
		const size_t &	Npred,
		RanIndex &	up,
		const string &	blkIndFileNam,
		const int &	nThr
	)

Constructor with a prior index.

The total number of predictors (columns in Xmat) is the provided number of predictors times the number of blocks. The file that has the block start indexes should be a white-space delimited text file. The file that has the lower level index information should have a matrix of _int with the number of rows the same as the number of rows in the data, and the number of columns equal to the number of blocks.

Parameters

[in]	Grp&	data for initialization
[in]	string&	name of the predictor file
[in]	size_t&	number of predictors per block
[in]	RanIndex&	prior (upper-level) index
[in]	string&	name of the file with the block indexes
[in]	int&	number of threads

◆ BetaBlk() [4/8]

BetaBlk::BetaBlk	(	const Grp &	dat,
		const string &	predFlName,
		const size_t &	Npred,
		RanIndex &	up,
		const string &	outFlNam,
		const string &	blkIndFileNam,
		const int &	nThr
	)

Constructor with a prior index and output file.

The total number of predictors (columns in Xmat) is the provided number of predictors times the number of blocks. The file that has the block start indexes should be a white-space delimited text file. The file that has the lower level index information should have a matrix of _int with the number of rows the same as the number of rows in the data, and the number of columns equal to the number of blocks.

Parameters

[in]	Grp&	data for initialization
[in]	string&	name of the predictor file
[in]	size_t&	number of predictors per block
[in]	RanIndex&	prior (upper-level) index
[in]	string&	output file name
[in]	string&	name of the file with the block indexes
[in]	int&	number of threads

◆ BetaBlk() [5/8]

BetaBlk::BetaBlk	(	const Grp &	dat,
		const string &	predFlName,
		const size_t &	Npred,
		const double &	absLab,
		const string &	blkIndFileNam,
		const int &	nThr
	)

Constructor with missing predictor data.

The total number of predictors (columns in Xmat) is the provided number of predictors times the number of blocks. The file that has the block start indexes should be a white-space delimited text file. The file that has the lower level index information should have a matrix of _int with the number of rows the same as the number of rows in the data, and the number of columns equal to the number of blocks.

Parameters

[in]	Grp&	data for initialization
[in]	string&	name of the predictor file
[in]	size_t&	number of predictors per block
[in]	double&	missing value label
[in]	string&	name of the file with the block indexes
[in]	int&	number of threads

◆ BetaBlk() [6/8]

BetaBlk::BetaBlk	(	const Grp &	dat,
		const string &	predFlName,
		const size_t &	Npred,
		const double &	absLab,
		const string &	outFlNam,
		const string &	blkIndFileNam,
		const int &	nThr
	)

Constructor with missing predictor values and output file name.

The total number of predictors (columns in Xmat) is the provided number of predictors times the number of blocks. The file that has the block start indexes should be a white-space delimited text file. The file that has the lower level index information should have a matrix of _int with the number of rows the same as the number of rows in the data, and the number of columns equal to the number of blocks.

Parameters

[in]	Grp&	data for initialization
[in]	string&	name of the predictor file
[in]	size_t&	number of predictors per block
[in]	double&	missing value label
[in]	string&	output file name
[in]	string&	name of the file with the block indexes
[in]	int&	number of threads

◆ BetaBlk() [7/8]

BetaBlk::BetaBlk	(	const Grp &	dat,
		const string &	predFlName,
		const size_t &	Npred,
		const double &	absLab,
		RanIndex &	up,
		const string &	blkIndFileNam,
		const int &	nThr
	)

Constructor with a prior index and missing predictor data.

The total number of predictors (columns in Xmat) is the provided number of predictors times the number of blocks. The file that has the block start indexes should be a white-space delimited text file. The file that has the lower level index information should have a matrix of _int with the number of rows the same as the number of rows in the data, and the number of columns equal to the number of blocks.

Parameters

[in]	Grp&	data for initialization
[in]	string&	name of the predictor file
[in]	size_t&	number of predictors per block
[in]	double&	missing data label
[in]	RanIndex&	prior (upper-level) index
[in]	string&	name of the file with the block indexes
[in]	int&	number of threads

◆ BetaBlk() [8/8]

BetaBlk::BetaBlk	(	const Grp &	dat,
		const string &	predFlName,
		const size_t &	Npred,
		const double &	absLab,
		RanIndex &	up,
		const string &	outFlNam,
		const string &	blkIndFileNam,
		const int &	nThr
	)

Constructor with a prior index, missing predictor data, and output file.

The total number of predictors (columns in Xmat) is the provided number of predictors times the number of blocks. The file that has the block start indexes should be a white-space delimited text file. The file that has the lower level index information should have a matrix of _int with the number of rows the same as the number of rows in the data, and the number of columns equal to the number of blocks.

Parameters

[in]	Grp&	data for initialization
[in]	string&	name of the predictor file
[in]	size_t&	number of predictors per block
[in]	double&	missing data label
[in]	RanIndex&	prior (upper-level) index
[in]	string&	output file name
[in]	string&	name of the file with the block indexes
[in]	int&	number of threads

Member Data Documentation

◆ _blkStart

vector< size_t > BetaBlk::_blkStart

protected

Block start indexes.

Vector of indexes that indicate the column that starts each block.

◆ _eachB

vector< gsl_matrix_view > BetaBlk::_eachB

protected

Regression coefficient submatrices.

A vector of GSL matrix views of the overall value matrix.

◆ _eachX

vector< gsl_matrix_view > BetaBlk::_eachX

protected

Predictor submatrices.

A vector of GSL matrix views of the submatrices of the overall predictor matrix that correspond to each trait block.

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

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BetaBlk() [1/8]

◆ BetaBlk() [2/8]

◆ BetaBlk() [3/8]

◆ BetaBlk() [4/8]

◆ BetaBlk() [5/8]

◆ BetaBlk() [6/8]

◆ BetaBlk() [7/8]

◆ BetaBlk() [8/8]

Member Data Documentation

◆ _blkStart

◆ _eachB

◆ _eachX