MuGen.h File Reference

C++ classes for hierarchical Bayesian Multi-trait quantitative-genetic models. More...

#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_permutation.h>
#include <vector>
#include <string>
#include <list>

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Classes
class	MVnorm
	The abstract base class for location parameter rows. More...
class	MVnormMu
	Individual vector of means. More...
class	MVnormMuPEX
	Individual vector of means with parameter expansion. More...
class	MVnormBetaPEX
	Individual regression with parameter expansion. More...
class	MVnormMuMiss
	Individual vector of means with missing data. More...
class	MVnormBeta
	Generic regression. More...
class	MVnormBetaFt
	Regression with multiple predictors. More...
class	MVnormMuBlk
	Individual vector of means with blocks of traits. More...
class	MVnormBetaBlk
	Individual vector of regression coefficients with blocks of traits. More...
class	MVnormBetaFtBlk
	Individual vector of conditional regression coefficients with blocks of traits. More...
class	RanIndex
	Generic index class. More...
class	RanIndexVS
	BVSR index class. More...
class	Apex
	Multiplicative redundant parameter. More...
class	Grp
	Base location parameter group class. More...
class	MuGrp
	Hierarchical mean. More...
class	MuGrpPEX
	"Random effect" with parameter expansion More...
class	MuGrpMiss
	Data with missing phenotype values. More...
class	MuGrpEE
	Data with measurement error. More...
class	MuGrpEEmiss
	Data with measurement error and missing phenotypes. More...
class	BetaGrpFt
	Multivariate multiple regression. More...
class	BetaGrpPEX
	Multivariate multiple regression with parameter expansion. More...
class	BetaGrpPC
	Relationship matrix regression. More...
class	BetaGrpPCpex
	Multiplicative parameter expansion for PC regression. More...
class	BetaGrpSnp
	Simple single-SNP regression class. More...
class	BetaGrpSnpCV
	Single-SNP regression with conditional variance. More...
class	BetaGrpPSR
	Single-SNP regression with partial effects. More...
class	BetaGrpSnpMiss
	Simple single-SNP regression class with missing data. More...
class	BetaGrpSnpMissCV
	Single-SNP regression with conditional variance and missing data. More...
class	BetaGrpPSRmiss
	Single-SNP regression with partial effects and missing data. More...
class	BetaGrpBVSR
	Bayesian variable selection regression. More...
class	MuBlk
	Hierarchical mean with independent blocks of traits. More...
class	BetaBlk
	Regression with independent blocks of traits. More...
class	SigmaI
	Basic inverse-covariance. More...
class	SigmaIblk
	Block-diagonal inverse-covariance. More...
class	SigmaIpex
	PEX inverse-covariance. More...
class	Qgrp
	Standard Student- \(t\) weights. More...
class	QgrpPEX
	Student- \(t\) weights for PEX. More...
class	MixP
	Dirichlet-multinomial mixture prior. More...

Functions
void	MVgauss (const gsl_vector *, const gsl_matrix *, const gsl_rng *, gsl_vector *)
	Multivariate Gaussian sampling function. More...
void	Wishart (const gsl_matrix *, const int &, const gsl_rng *, gsl_matrix *)
void	Wishart (const gsl_matrix *, const size_t &, const gsl_rng *, gsl_matrix *)
size_t	rtgeom (const double &, const size_t &, const gsl_rng *)
	Truncated geometric distribution. More...
double	mhl (const gsl_vector *beta, const gsl_matrix *SigI)
	Mahalanobis distance. More...
void	colCenter (gsl_matrix *inplace)
	Matrix centering in-place. More...
void	colCenter (const gsl_matrix *source, gsl_matrix *res)
	Matrix centering with copy. More...
void	colCenter (gsl_matrix *inplace, const double &absLab)
	Matrix centering in-place with missing values. More...
void	colCenter (const gsl_matrix *source, gsl_matrix *res, const double &absLab)
	Matrix centering with copy and missing values. More...
void	vecCenter (gsl_vector *inplace)
	Vector centering in-place. More...
void	vecCenter (const gsl_vector *source, gsl_vector *res)
	Vector centering with copy. More...
void	meanImpute (gsl_matrix *inplace, const double &absLab)
	Mean imputation without centering. More...
void	printMat (const gsl_matrix *m)
	Print matrix to screen. More...
unsigned long long	rdtsc ()
	Accessing the processor RTDSC instruction. More...
MuGrp	operator+ (const Grp &m1, const Grp &m2)
	Addition operator. More...
MuGrp	operator+ (const MuGrp &m1, const Grp &m2)
	Addition operator. More...
MuGrp	operator+ (const Grp &m1, const MuGrp &m2)
	Addition operator. More...
MuGrp	operator- (const Grp &m1, const Grp &m2)
	Subtraction operator. More...
MuGrp	operator- (const MuGrp &m1, const Grp &m2)
	Subtraction operator. More...
MuGrp	operator- (const Grp &m1, const MuGrp &m2)
	Subtraction operator. More...

Detailed Description

C++ classes for hierarchical Bayesian Multi-trait quantitative-genetic models.

Author

Anthony J. Greenberg

Copyright

Copyright (c) 2015 Anthony J. Greenberg

Version

0.9.1

This is the project header file containing class definitions and interface documentation.