Individual vector of means with missing data. More...

#include <MuGen.h>

Inheritance diagram for MVnormMuMiss:

Collaboration diagram for MVnormMuMiss:

Public Member Functions
	MVnormMuMiss ()
	Default constructor.

	MVnormMuMiss (const size_t &d)
	0-mean deterministic constructor More...

	MVnormMuMiss (const size_t &d, const vector< size_t > &low, const size_t &up, const vector< size_t > &mis)
	Deterministic constructor. More...

	MVnormMuMiss (gsl_vector *mn, const vector< size_t > &low, const size_t &up, const vector< size_t > &mis)
	Deterministic constructor with a vector. More...

	MVnormMuMiss (gsl_vector *mn, const size_t &up, const vector< size_t > &mis)
	Deterministic constructor with a vector. More...

	MVnormMuMiss (gsl_vector mn, const gsl_vector sd, const gsl_rng *r, const vector< size_t > &low, const size_t &up, const vector< size_t > &mis)
	Univariate random constructor with a vector. More...

	MVnormMuMiss (gsl_vector mn, const gsl_matrix Sig, const gsl_rng *r, const vector< size_t > &low, const size_t &up, const vector< size_t > &mis)
	Multivariate random constructor with a vector. More...

	MVnormMuMiss (gsl_matrix *mn, const size_t &iRw, const vector< size_t > &low, const size_t &up, const vector< size_t > &mis)
	Deterministic constructor with a matrix. More...

	MVnormMuMiss (gsl_matrix *mn, const size_t &iRw, const size_t &up, const vector< size_t > &mis)
	Deterministic constructor with a matrix. More...

	MVnormMuMiss (gsl_matrix mn, const size_t &iRw, const gsl_vector sd, const gsl_rng *r, const vector< size_t > &low, const size_t &up, const vector< size_t > &mis)
	Univariate random constructor with a matrix. More...

	MVnormMuMiss (gsl_matrix mn, const size_t &iRw, const gsl_matrix Sig, const gsl_rng *r, const vector< size_t > &low, const size_t &up, const vector< size_t > &mis)
	Multivariate random constructor with a matrix. More...

	MVnormMuMiss (const MVnormMuMiss &)
	Deterministic copy constructor. More...

MVnormMuMiss &	operator= (const MVnormMuMiss &)
	Assignment operator. More...

	~MVnormMuMiss ()
	Destructor.

void	update (const Grp &mu, const SigmaI &SigIm, const gsl_rng *r)
	Gaussian likelihood. More...

void	update (const Grp &mu, const SigmaI &SigIm, const SigmaI &SigIp, const gsl_rng *r)
	Gaussian likelihood, Gaussian 0-mean prior. More...

size_t	nMissP () const
	Number of missing values. More...

const vector< size_t >	getMisPhen () const
	Indexes of missing values. More...

Public Member Functions inherited from MVnormMu
	MVnormMu ()
	Default constructor. More...

	MVnormMu (const size_t &d)
	Zero vector constructor. More...

	MVnormMu (const size_t &d, const vector< size_t > &low, const size_t &up)
	Zero vector with pointers. More...

	MVnormMu (gsl_vector *mn, const vector< size_t > &low, const size_t &up)
	Deterministic constructor. More...

	MVnormMu (gsl_vector *mn, const size_t &up)
	Deterministic constructor, prior index only. More...

	MVnormMu (gsl_matrix *mn, const size_t &iRw)
	Deterministic constructor with a matrix. More...

	MVnormMu (gsl_matrix *mn, const size_t &iRw, const vector< size_t > &low)
	Deterministic constructor with a matrix and an index to data. More...

	MVnormMu (gsl_matrix *mn, const size_t &iRw, const vector< size_t > &low, const size_t &up)
	Deterministic constructor with a matrix and indexes to data and a prior. More...

	MVnormMu (gsl_matrix *mn, const size_t &iRw, const size_t &up)
	Deterministic constructor with a matrix and an index to a prior. More...

	MVnormMu (gsl_vector mn, const gsl_vector sd, const gsl_rng *r, const vector< size_t > &low, const size_t &up)
	Univariate random constructor with a vector and indexes to data and a prior. More...

	MVnormMu (gsl_vector mn, const gsl_matrix Sig, const gsl_rng *r, const vector< size_t > &low, const size_t &up)
	Multivariate random constructor with a vector and indexes to data and a prior. More...

	MVnormMu (gsl_matrix mn, const size_t &iRw, const gsl_vector sd, const gsl_rng *r, const vector< size_t > &low, const size_t &up)
	Univariate random constructor with a matrix and indexes to data and a prior. More...

	MVnormMu (gsl_matrix mn, const size_t &iRw, const gsl_matrix Sig, const gsl_rng *r, const vector< size_t > &low, const size_t &up)
	Multivariate random constructor with a matrix and indexes to data and a prior. More...

	MVnormMu (const MVnormMu &)
	Copy constructor. More...

MVnormMu &	operator= (const MVnormMu &)
	Assignment operator. More...

virtual	~MVnormMu ()
	Destructor.

virtual void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm, const gsl_rng *r)
	Sudent- \(t\) likelihood. More...

virtual void	update (const Grp &dat, const SigmaI &SigIm, const double &qPr, const SigmaI &SigIp, const gsl_rng *r)
	Gaussian likelihood, Student- \(t\) prior. More...

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

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

virtual void	update (const Grp &dat, const SigmaI &SigIm, const Grp &muPr, const SigmaI &SigIp, const gsl_rng *r)
	Gaussian likelihood, Gaussian prior. More...

virtual void	update (const Grp &dat, const SigmaI &SigIm, const Grp &muPr, const double &qPr, const SigmaI &SigIp, const gsl_rng *r)
	Gaussian likelihood, Student- \(t\) prior. More...

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

virtual void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm, const Grp &muPr, const double &qPr, const SigmaI &SigIp, const gsl_rng *r)
	Student- \(t\) likelihood, Student- \(t\) prior. More...

const vector< size_t > *	down () const
	Points to the corresponding data. More...

const size_t *	up () const
	Points to the prior. More...

Public Member Functions inherited from MVnorm
	MVnorm (const MVnorm &)
	Copy constructor. More...

MVnorm &	operator= (const MVnorm &)
	Assignement operator. More...

virtual	~MVnorm ()
	Virtual destructor. More...

virtual double	mhl (const MVnorm *x, const SigmaI &SigI)
	Mahalanobis distance to a vector. More...

virtual double	mhl (const MVnorm *x, const SigmaI &SigI) const
	Mahalanobis distance to a vector. More...

virtual double	mhl (const gsl_vector *x, const SigmaI &SigI)
	Mahalanobis distance to a vector. More...

virtual double	mhl (const gsl_vector *x, const SigmaI &SigI) const
	Mahalanobis distance to a vector. More...

virtual double	mhl (const SigmaI &SigI)
	Mahalanobis distance to zero. More...

virtual double	mhl (const SigmaI &SigI) const
	Mahalanobis distance to zero. More...

double	density (const gsl_vector *theta, const SigmaI &SigI)
	Multivariate Gaussian density. More...

double	density (const gsl_vector *theta, const SigmaI &SigI) const
	Multivariate Gaussian density. More...

double	density (const MVnorm *theta, const SigmaI &SigI)
	Multivariate Gaussian density. More...

double	density (const MVnorm *theta, const SigmaI &SigI) const
	Multivariate Gaussian density. More...

void	save (const string &fileNam, const char *how="a")
	Save function. More...

void	save (FILE *fileStr)
	Save function. More...

double	operator[] (const size_t i) const
	Subscript operator. More...

void	valSet (const size_t i, const double x)
	Setting an element to a value. More...

const gsl_vector *	getVec () const
	Access the location vector. More...

size_t	len () const
	Length of the location vector. More...

virtual double	scalePar () const
	Scale parameter. More...

Protected Attributes
vector< size_t >	_misPhenInd
	Missing data index. More...

size_t	_myInd
	own index More...

Protected Attributes inherited from MVnormMu
const vector< size_t > *	_lowLevel
	Data indexes. More...

const size_t *	_upLevel
	Prior index. More...

Protected Attributes inherited from MVnorm
gsl_vector_view	_vec
	Data vector. More...

size_t	_d
	Length of the data vector.

Additional Inherited Members
Protected Member Functions inherited from MVnorm
	MVnorm ()
	Default constructor. More...

	MVnorm (const size_t &d)
	Dimension-only constructor. More...

	MVnorm (gsl_vector *mn)
	Dimension and vector value constructor. More...

	MVnorm (gsl_vector mn, const gsl_vector sd, const gsl_rng *r)
	Univariate Gaussian constructor. More...

	MVnorm (gsl_vector mn, const gsl_matrix Sig, const gsl_rng *r)
	Multivariate Gaussian constructor. More...

	MVnorm (gsl_matrix *mn, const size_t &iRw)
	Dimension and vector value constructor. More...

	MVnorm (gsl_matrix mn, const size_t &iRw, const gsl_vector sd, const gsl_rng *r)
	Univariate Gaussian constructor with a matrix. More...

	MVnorm (gsl_matrix mn, const size_t &iRw, const gsl_matrix Sig, const gsl_rng *r)
	Multivariate Gaussian constructor with a matrix. More...

Detailed Description

Individual vector of means with missing data.

Implements missing phenotype data imputation. Some parameters for update methods have a different meaning than for other MVnorm classes.

Constructor & Destructor Documentation

◆ MVnormMuMiss() [1/11]

MVnormMuMiss::MVnormMuMiss ( const size_t & d )

inline

0-mean deterministic constructor

Sets up the instance to point to a vector of zeros

Parameters

[in] size_t& dimension of the vector

◆ MVnormMuMiss() [2/11]

MVnormMuMiss::MVnormMuMiss	(	const size_t &	d,
		const vector< size_t > &	low,
		const size_t &	up,
		const vector< size_t > &	mis
	)

Deterministic constructor.

Parameters

[in]	size_t&	dimension of the vector
[in]	vector<size_t>&	vector of row indexes for data
[in]	size_t&	row index for the prior matrix
[in]	vector<size_t>&	indexes of missing data

◆ MVnormMuMiss() [3/11]

MVnormMuMiss::MVnormMuMiss	(	gsl_vector *	mn,
		const vector< size_t > &	low,
		const size_t &	up,
		const vector< size_t > &	mis
	)

Deterministic constructor with a vector.

Parameters

[in]	gsl_vector*	vector of values
[in]	size_t&	dimension of the vector
[in]	vector<size_t>&	vector of row indexes for data
[in]	size_t&	row index for the prior matrix
[in]	vector<size_t>&	indexes of missing data

◆ MVnormMuMiss() [4/11]

MVnormMuMiss::MVnormMuMiss	(	gsl_vector *	mn,
		const size_t &	up,
		const vector< size_t > &	mis
	)

Deterministic constructor with a vector.

Parameters

[in]	gsl_vector*	vector of values
[in]	size_t&	row index for the prior matrix
[in]	vector<size_t>&	indexes of missing data

◆ MVnormMuMiss() [5/11]

MVnormMuMiss::MVnormMuMiss	(	gsl_vector *	mn,
		const gsl_vector *	sd,
		const gsl_rng *	r,
		const vector< size_t > &	low,
		const size_t &	up,
		const vector< size_t > &	mis
	)

Univariate random constructor with a vector.

Parameters

[in]	gsl_vector*	vector of values
[in]	gsl_vector*	vector of standard deviations
[in]	gsl_rng*	pointer to a PNG
[in]	size_t&	dimension of the vector
[in]	vector<size_t>&	vector of row indexes for data
[in]	size_t&	row index for the prior matrix
[in]	vector<size_t>&	indexes of missing data

◆ MVnormMuMiss() [6/11]

MVnormMuMiss::MVnormMuMiss	(	gsl_vector *	mn,
		const gsl_matrix *	Sig,
		const gsl_rng *	r,
		const vector< size_t > &	low,
		const size_t &	up,
		const vector< size_t > &	mis
	)

Multivariate random constructor with a vector.

Parameters

[in]	gsl_vector*	vector of values
[in]	gsl_matrix*	covariance matrix
[in]	gsl_rng*	pointer to a PNG
[in]	size_t&	dimension of the vector
[in]	vector<size_t>&	vector of row indexes for data
[in]	size_t&	row index for the prior matrix
[in]	vector<size_t>&	indexes of missing data

◆ MVnormMuMiss() [7/11]

MVnormMuMiss::MVnormMuMiss	(	gsl_matrix *	mn,
		const size_t &	iRw,
		const vector< size_t > &	low,
		const size_t &	up,
		const vector< size_t > &	mis
	)

Deterministic constructor with a matrix.

Parameters

[in]	gsl_matrix*	vector of values
[in]	size_t&	row index of the matrix of values
[in]	vector<size_t>&	vector of row indexes for data
[in]	size_t&	row index for the prior matrix
[in]	vector<size_t>&	indexes of missing data

◆ MVnormMuMiss() [8/11]

MVnormMuMiss::MVnormMuMiss	(	gsl_matrix *	mn,
		const size_t &	iRw,
		const size_t &	up,
		const vector< size_t > &	mis
	)

Deterministic constructor with a matrix.

Parameters

[in]	gsl_matrix*	vector of values
[in]	size_t&	row index of the matrix of values
[in]	size_t&	row index for the prior matrix
[in]	vector<size_t>&	indexes of missing data

◆ MVnormMuMiss() [9/11]

MVnormMuMiss::MVnormMuMiss	(	gsl_matrix *	mn,
		const size_t &	iRw,
		const gsl_vector *	sd,
		const gsl_rng *	r,
		const vector< size_t > &	low,
		const size_t &	up,
		const vector< size_t > &	mis
	)

Univariate random constructor with a matrix.

Parameters

[in]	gsl_matrix*	matrix of values
[in]	size_t&	row index of the matrix of values
[in]	gsl_vector*	vector of standard deviations
[in]	gsl_rng*	pointer to a PNG
[in]	size_t&	dimension of the vector
[in]	vector<size_t>&	vector of row indexes for data
[in]	size_t&	row index for the prior matrix
[in]	vector<size_t>&	indexes of missing data

◆ MVnormMuMiss() [10/11]

MVnormMuMiss::MVnormMuMiss	(	gsl_matrix *	mn,
		const size_t &	iRw,
		const gsl_matrix *	Sig,
		const gsl_rng *	r,
		const vector< size_t > &	low,
		const size_t &	up,
		const vector< size_t > &	mis
	)

Multivariate random constructor with a matrix.

Parameters

[in]	gsl_matrix*	matrix of values
[in]	size_t&	row index of the matrix of values
[in]	gsl_matrix*	covariance matrix
[in]	gsl_rng*	pointer to a PNG
[in]	size_t&	dimension of the vector
[in]	vector<size_t>&	vector of row indexes for data
[in]	size_t&	row index for the prior matrix
[in]	vector<size_t>&	indexes of missing data

◆ MVnormMuMiss() [11/11]

MVnormMuMiss::MVnormMuMiss ( const MVnormMuMiss & )

Deterministic copy constructor.

Parameters

[in] MVnormMuMiss& object of type MVnormMuMiss

Member Function Documentation

◆ getMisPhen()

const vector<size_t> MVnormMuMiss::getMisPhen ( ) const

inlinevirtual

Indexes of missing values.

Accesses a vector with indexes of missing phenotypes. Implemented for this class.

Returns: Vector of size_t that contains indexes that correspond to missing values.

Reimplemented from MVnormMu.

◆ nMissP()

size_t MVnormMuMiss::nMissP ( ) const

inlinevirtual

Number of missing values.

Accesses the number of missing phenotype values. Implemented in this class.

Returns: Number of missing phenotypes, of type size_t.

Reimplemented from MVnormMu.

◆ operator=()

MVnormMuMiss& MVnormMuMiss::operator= ( const MVnormMuMiss & )

Assignment operator.

Deterministic assignement operator

Parameters

[in] MVnormMuMiss& object of type MVnormMuMiss

Returns: A reference to an object of type MVnormMuMiss

◆ update() [1/2]

void MVnormMuMiss::update	(	const Grp &	mu,
		const SigmaI &	SigIm,
		const gsl_rng *	r
	)

virtual

Gaussian likelihood.

Here, the Grp variable contains the means for imputation rather than the data

Parameters

[in]	Grp&	data
[in]	SigmaI&	inverse-covariance matrix for the likelihood
[in]	gsl_rng*	pointer to a PNG

Reimplemented from MVnormMu.

◆ update() [2/2]

void MVnormMuMiss::update	(	const Grp &	mu,
		const SigmaI &	SigIm,
		const SigmaI &	SigIp,
		const gsl_rng *	r
	)

virtual

Gaussian likelihood, Gaussian 0-mean prior.

Here, the Grp variable contains the means for imputation rather than the data

Parameters

[in]	Grp&	data
[in]	SigmaI&	inverse-covariance matrix for the likelihood
[in]	SigmaI&	inverse-covariance matrix for the prior
[in]	gsl_rng*	pointer to a PNG

Reimplemented from MVnormMu.

Member Data Documentation

◆ _misPhenInd

vector<size_t> MVnormMuMiss::_misPhenInd

protected

Missing data index.

Vector of indexes tagging missing data.

◆ _myInd

size_t MVnormMuMiss::_myInd

protected

own index

Index of the row the current instance of this class is pointing to. Only defined with constructors that take iRw.

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

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MVnormMuMiss() [1/11]

◆ MVnormMuMiss() [2/11]

◆ MVnormMuMiss() [3/11]

◆ MVnormMuMiss() [4/11]

◆ MVnormMuMiss() [5/11]

◆ MVnormMuMiss() [6/11]

◆ MVnormMuMiss() [7/11]

◆ MVnormMuMiss() [8/11]

◆ MVnormMuMiss() [9/11]

◆ MVnormMuMiss() [10/11]

◆ MVnormMuMiss() [11/11]

Member Function Documentation

◆ getMisPhen()

◆ nMissP()

◆ operator=()

◆ update() [1/2]

◆ update() [2/2]

Member Data Documentation

◆ _misPhenInd

◆ _myInd