Data with missing phenotype values. More...

#include <MuGen.h>

Inheritance diagram for MuGrpMiss:

Collaboration diagram for MuGrpMiss:

Public Member Functions
	MuGrpMiss ()
	Default constructor.

	MuGrpMiss (const string &datFlNam, const string &misMatFlNam, const string &misVecFlNam, RanIndex &up, const size_t &d)
	Full constructor. More...

	~MuGrpMiss ()
	Destructor.

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

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

virtual void	update (const Grp &mu, const SigmaI &SigIm)
	Standard Gaussian imputation. More...

virtual void	update (const Grp &mu, const SigmaI &SigIm, const SigmaI &SigIp)
	Gaussian imputation with a prior. More...

size_t	nMis () const

size_t	nMis ()

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

	MuGrp (RanIndex &low, const size_t &d)
	Deterministic zero-value constructor. More...

	MuGrp (const string &datFlNam, RanIndex &low, RanIndex &up, const size_t &d)
	Constructor with data from file. More...

	MuGrp (const string &datFlNam, RanIndex &up, const size_t &d)
	Constructor with data from file and no lower level. More...

	MuGrp (const vector< MVnorm * > &dat, RanIndex &low, RanIndex &up)
	Constructor with a vector of MVnorm pointers. More...

	MuGrp (const Grp &dat, RanIndex &low, RanIndex &up)
	Constructor with a Grp object. More...

	MuGrp (const vector< MVnorm * > &dat, RanIndex &low, RanIndex &up, const string &outFlNam)
	Constructor with a vector of MVnorm pointers and output file name. More...

	MuGrp (const Grp &dat, RanIndex &low, RanIndex &up, const string &outFlNam)
	Constructor with a Grp object and output file name. More...

	MuGrp (const Grp &dat, RanIndex &low)
	Deterministic mean constructor. More...

	MuGrp (const Grp &dat, const Qgrp &q, RanIndex &low)
	Deterministic weighted mean constructor. More...

	MuGrp (const gsl_matrix *dat)
	Deterministic constructor with a GSL matrix. More...

	MuGrp (const gsl_matrix *dat, RanIndex &low)
	Deterministic GSL matrix mean constructor. More...

	MuGrp (const gsl_matrix *dat, const Qgrp &q, RanIndex &low)
	Deterministic GSL matrix weighted mean constructor. More...

virtual	~MuGrp ()
	Destructor.

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

	MuGrp (const Grp &g)
	Copy constructor. More...

MuGrp &	operator= (const MuGrp &mG)
	Assignemnt operator. More...

virtual void	update (const Grp &dat, const Qgrp &q, const SigmaI &SigIm)
	Student- \(t\) likelihood, improper 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 SigmaI &SigI)
	Save with inverse-covariance. 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...

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

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

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

virtual const gsl_matrix *	fMat () 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...

virtual double	lnOddsRat (const Grp &y, const SigmaI &SigI, const size_t i) const
	Log-odds ratio. 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 Attributes
vector< size_t >	_misInd
	Index of the rows with missing data.

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.

Additional Inherited Members
Protected Member Functions inherited from Grp
	Grp ()

Detailed Description

Data with missing phenotype values.

Implements missing phenotypic (responce) data imputation. This object has to be at the bottom of the hierarchy, so there is no index to the lower level.

Constructor & Destructor Documentation

◆ MuGrpMiss() [1/2]

MuGrpMiss::MuGrpMiss	(	const string &	datFlNam,
		const string &	misMatFlNam,
		const string &	misVecFlNam,
		RanIndex &	up,
		const size_t &	d
	)

Full constructor.

Reads data and indexes that show which data are missing from files. Matrix index has the same dimensions as the value matrix and has "1" in places where the data are missing and "0" otherwise. The vector missing data index indicates the number of data points missing in each row (zero for rows with all data present). The data file can have any double-precision value in place of missing data. These values are ignored and replaced by the overall mean at construction, but subsequently updated.

Parameters

[in]	string&	data file name
[in]	string&	matrix missing data index file name
[in]	string&	vector missing data index file name
[in]	RanIndex&	index pointing to the prior (next level in the hierarchy)
[in]	size_t&	number of traits

◆ MuGrpMiss() [2/2]

MuGrpMiss::MuGrpMiss ( const MuGrpMiss & mG )

Copy constructor.

Parameters

[in] MuGrpMiss& object to be copied

Returns: MuGrpMiss object

Member Function Documentation

◆ operator=()

MuGrpMiss & MuGrpMiss::operator= ( const MuGrpMiss & mG )

Assignment operator.

Parameters

[in] MuGrpMiss& object to be copied

Returns: MuGrpMiss& target object

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

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MuGrpMiss() [1/2]

◆ MuGrpMiss() [2/2]

Member Function Documentation

◆ operator=()