MuGen  0.9.1
Multi-trait hierarchical quantitative genetic models
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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
Version
0.9.1

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