# Bayesian Methods and Graphical Model Structures for Statistical Modeling

## Documentation for package ‘bbricks’ version 0.1.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

B C D F G H I L M P R S misc

## -- B --

BasicBayesian | Create objects of type '"BasicBayesian"'.

## -- C --

cancerData | Cancer mortality of 20 cities
CatDirichlet | Create objects of type "CatDirichlet".
CatDP | Create objects of type "CatDP".
CatHDP | Create objects of type "CatHDP".
CatHDP2 | Create objects of type "CatHDP2".

## -- D --

dAllIndicators | Get the probabilities of all possible values of the hidden indicator variables from the DP family objects.
dAllIndicators.HDP | Get the probabilities of all possible values of the hidden indicator variables of an "HDP" object.
dCategorical | Probability mass function for Categorical distribution
dDir | Density function for Dirichelt distribution
dGaussian | Density function of Gaussian distribution
dInvGamma | Density function of Inverse-Gamma distribution
dInvWishart | Density function of Inverse-Wishart distribution
dNIW | Density function for Normal-Inverse-Wishart (NIW) distribution.
DP | Create objects of type "DP".
dPosterior | Get the density from the posterior distribution.
dPosterior.CatDirichlet | Density function of the posterior distribution of a "CatDirichlet" object
dPosterior.GaussianGaussian | Density function of the posterior distribution of a "GaussianGaussian" object
dPosterior.GaussianInvWishart | Density function of the posterior distribution of a "GaussianInvWishart" object
dPosterior.GaussianNIG | Density function of the posterior distribution of a "GaussianNIG" object
dPosterior.GaussianNIW | Density function of the posterior distribution of a "GaussianNIW" object
dPosterior.LinearGaussianGaussian | Posterior density function of a "LinearGaussianGaussian" object
dPosteriorPredictive | Get the density value of the posterior predictive distribution
dPosteriorPredictive.CatDirichlet | Posterior predictive density function of a "CatDirichlet" object
dPosteriorPredictive.CatDP | Posterior predictive density function of a "CatDP" object
dPosteriorPredictive.CatHDP | Posterior predictive density function of a "CatHDP" object
dPosteriorPredictive.CatHDP2 | Posterior predictive density function of a "CatHDP" object
dPosteriorPredictive.DP | Posterior predictive density function of a Dirichlet Process object
dPosteriorPredictive.GaussianGaussian | Posterior predictive density function of a "GaussianGaussian" object
dPosteriorPredictive.GaussianInvWishart | Posterior predictive density function of a "GaussianInvWishart" object
dPosteriorPredictive.GaussianNIG | Posterior predictive density function of a "GaussianNIG" object
dPosteriorPredictive.GaussianNIW | Posterior predictive density function of a "GaussianNIW" object
dPosteriorPredictive.HDP | Posterior predictive density function of a "HDP" object
dPosteriorPredictive.HDP2 | Posterior predictive density function of a "HDP2" object
dPosteriorPredictive.LinearGaussianGaussian | Posterior predictive density function of a "LinearGaussianGaussian" object
dT | Density function for (multivariate) t distribution
dWishart | Density function of Wishart distribution

## -- F --

farmadsData | farm ads data

## -- G --

GaussianGaussian | Create objects of type "GaussianGaussian".
GaussianInvWishart | Create objects of type "GaussianInvWishart".
GaussianNIG | Create objects of type "GaussianNIG".
GaussianNIW | Create objects of type "GaussianNIW".

## -- H --

HDP | Create objects of type "HDP".
HDP2 | Create objects of type "HDP2".
hlrData | Samples from a hierarchical linear model
hmmData | Samples from a hidden Markov model

## -- I --

inferenceJointGaussian | Inference in joint Gaussian distribution

## -- L --

LinearGaussianGaussian | Create objects of type "LinearGaussianGaussian".
logsumexp | log sum exp
lrData | Samples from a simple linear model

## -- M --

MAP | Get the Maximum A Posteriori(MAP) estimate of a "BayesianBrick" object
MAP.CatDirichlet | MAP estimate of a "CatDirichlet" object
MAP.CatDP | Maximum A Posteriori(MAP) estimate of a "CatDP" object
MAP.GaussianGaussian | Maximum A Posteriori (MAP) estimate of a "GaussianGaussian" object
MAP.GaussianInvWishart | Maximum A Posteriori (MAP) estimate of a "GaussianInvWishart" object
MAP.GaussianNIG | Maximum A Posteriori (MAP) estimate of a "GaussianNIG" object
MAP.GaussianNIW | Maximum A Posteriori (MAP) estimate of a "GaussianNIW" object
MAP.LinearGaussianGaussian | Maximum A Posteriori (MAP) estimate of a "LinearGaussianGaussian" object
marginalLikelihood | Get the marginal likelihood of a "BayesianBrick" object
marginalLikelihood.CatDirichlet | Marginal likelihood of a "CatDirichlet" object
marginalLikelihood.CatDP | Marginal likelihood of a "CatDP" object
marginalLikelihood.DP | Marginal likelihood for Dirichlet Process(DP)
marginalLikelihood.GaussianGaussian | Marginal likelihood of a "GaussianGaussian" object
marginalLikelihood.GaussianInvWishart | Marginal likelihood of a "GaussianInvWishart" object
marginalLikelihood.GaussianNIG | Marginal likelihood of a "GaussianNIG" object
marginalLikelihood.GaussianNIW | Marginal likelihood of a "GaussianNIW" object
marginalLikelihood.HDP | Marginal likelihood for HDP
marginalLikelihood.HDP2 | Marginal likelihood for HDP2
marginalLikelihood.LinearGaussianGaussian | Marginal likelihood of a "LinearGaussianGaussian" object
marginalLikelihood_bySufficientStatistics | Get the marginal likelihood of a "BayesianBrick" object
marginalLikelihood_bySufficientStatistics.CatDirichlet | Marginal likelihood of a "CatDirichlet" object, using sufficient statistics
marginalLikelihood_bySufficientStatistics.CatDP | Marginal likelihood of a "CatDP" object, using sufficient statistics
marginalLikelihood_bySufficientStatistics.GaussianGaussian | Marginal likelihood of a "GaussianGaussian" object, using sufficient statistics
marginalLikelihood_bySufficientStatistics.GaussianInvWishart | Marginal likelihood of a "GaussianInvWishart" object, using sufficient statistics
marginalLikelihood_bySufficientStatistics.GaussianNIG | Marginal likelihood of a "GaussianNIG" object, using sufficient statistics
marginalLikelihood_bySufficientStatistics.GaussianNIW | Marginal likelihood of a "GaussianNIW" object, using sufficient statistics
marginalLikelihood_bySufficientStatistics.LinearGaussianGaussian | Marginal likelihood of a "LinearGaussianGaussian" object, using sufficient statistics
MetropolisHastings | Metropolis-Hastings sampler
mmData | Samples from a mixture model
mmhData | Samples from a hierarchical mixture model
mmhhData | Samples from a hierarchical mixture model with two layers of hierarchies
MPE | Get the Mean Posterior Estimate(MPE) of a "BayesianBrick" object
MPE.CatDirichlet | MPE of a "CatDirichlet" object
MPE.CatDP | Mean Posterior Estimate(MPE) of a "CatDP" object
MPE.GaussianGaussian | Mean Posterior Estimate (MPE) of a "GaussianGaussian" object
MPE.GaussianInvWishart | Mean Posterior Estimate (MPE) of a "GaussianInvWishart" object
MPE.GaussianNIG | Mean Posterior Estimate (MPE) of a "GaussianNIG" object
MPE.GaussianNIW | Mean Posterior Estimate (MPE) of a "GaussianNIW" object
MPE.LinearGaussianGaussian | Mean Posterior Estimate (MPE) of a "LinearGaussianGaussian" object

## -- P --

pdsDeterminant | determinant of a positive definite symmetric matrix
pdsInverse | Inverse of a positive definite symmetric matrix
posterior | update the prior distribution with sufficient statistics
posterior.CatDirichlet | Update a "CatDirichlet" object with sample sufficient statistics
posterior.CatDP | Update a "CatDP" object with sample sufficient statistics
posterior.CatHDP | Update a "CatHDP" object with sample sufficient statistics
posterior.CatHDP2 | Update a "CatHDP2" object with sample sufficient statistics
posterior.DP | Update a "DP" object with sample sufficient statistics
posterior.GaussianGaussian | Update a "GaussianGaussian" object with sample sufficient statistics
posterior.GaussianInvWishart | Update a "GaussianInvWishart" object with sample sufficient statistics
posterior.GaussianNIG | Update a "GaussianNIG" object with sample sufficient statistics
posterior.GaussianNIW | Update a "GaussianNIW" object with sample sufficient statistics
posterior.HDP | Update a "HDP" object with sample sufficient statistics
posterior.HDP2 | Update a "HDP2" object with sample sufficient statistics
posterior.LinearGaussianGaussian | Update a "LinearGaussianGaussian" object with sample sufficient statistics
posteriorDiscard | update the prior distribution with sufficient statistics
posteriorDiscard.CatDirichlet | Update a "CatDirichlet" object with sample sufficient statistics
posteriorDiscard.CatDP | Update a "CatDP" object with sample sufficient statistics
posteriorDiscard.CatHDP | Update a "CatHDP" object with sample sufficient statistics
posteriorDiscard.CatHDP2 | Update a "CatHDP2" object with sample sufficient statistics
posteriorDiscard.DP | Update a "DP" object with sample sufficient statistics
posteriorDiscard.GaussianGaussian | Update a "GaussianGaussian" object with sample sufficient statistics
posteriorDiscard.GaussianInvWishart | Update a "GaussianInvWishart" object with sample sufficient statistics
posteriorDiscard.GaussianNIG | Update a "GaussianNIG" object with sample sufficient statistics
posteriorDiscard.GaussianNIW | Update a "GaussianNIW" object with sample sufficient statistics
posteriorDiscard.HDP | Update a "HDP" object with sample sufficient statistics
posteriorDiscard.HDP2 | Update a "HDP2" object with sample sufficient statistics
posteriorDiscard.LinearGaussianGaussian | Update a "LinearGaussianGaussian" object with sample sufficient statistics
posteriorDiscard_bySufficientStatistics | update the prior distribution with sufficient statistics
posteriorDiscard_bySufficientStatistics.CatDirichlet | Update the prior Dirichlet distribution with sample sufficient statistics
posteriorDiscard_bySufficientStatistics.CatDP | Update a "CatDP" object with sample sufficient statistics
posterior_bySufficientStatistics | update the prior distribution with sufficient statistics
posterior_bySufficientStatistics.CatDirichlet | Update a "CatDirichlet" object with sample sufficient statistics
posterior_bySufficientStatistics.CatDP | Update a "CatDP" object with sample sufficient statistics
print.BasicBayesian | Print the content of an BasicBayesian object
print.CatHDP | Print the content of an CatHDP object
print.CatHDP2 | Print the content of an CatHDP2 object
print.DP | print the content of a "DP" object
print.HDP | print the content of a "HDP" object
print.HDP2 | print the content of a "HDP2" object

## -- R --

rCategorical | Random generation for Categorical distribution
rDir | Random generation for Dirichelt distribution
release_questions | additional release questions
rGaussian | Random generation for Gaussian distribution
rInvGamma | Random number generation of Inverse-Gamma distribution
rInvWishart | Random generation for Inverse-Wishart distribution
rNIW | Random number generation for Normal-Inverse-Wishart (NIW) distribution.
rPosterior | Generate random samples from the posterior distribution
rPosterior.CatDirichlet | Generate ramdom samples from the posterior distribution of a "CatDirichlet" object
rPosterior.GaussianGaussian | Generate ramdom samples from the posterior distribution of a "GaussianGaussian" object
rPosterior.GaussianInvWishart | Generate one ramdom sample from the posterior distribution of a "GaussianInvWishart" object
rPosterior.GaussianNIG | Generate ramdom samples from the posterior distribution of a "GaussianNIG" object
rPosterior.GaussianNIW | Generate ramdom samples from the posterior distribution of a "GaussianNIW" object
rPosterior.LinearGaussianGaussian | Posterior random generation of a "LinearGaussianGaussian" object
rPosteriorPredictive | Generate random samples from the posterior predictive distribution
rPosteriorPredictive.CatDirichlet | Generate random samples from the posterior predictive distribution of a "CatDirichlet" object
rPosteriorPredictive.CatDP | Generate random samples from the posterior predictive distribution of a "CatDP" object
rPosteriorPredictive.CatHDP | Generate random samples from the posterior predictive distribution of a "CatHDP" object
rPosteriorPredictive.CatHDP2 | Generate random samples from the posterior predictive distribution of a "CatHDP2" object
rPosteriorPredictive.DP | Generate random samples from the posterior predictive distribution of a "DP" object
rPosteriorPredictive.GaussianGaussian | Generate random samples from the posterior predictive distribution of a "GaussianGaussian" object
rPosteriorPredictive.GaussianInvWishart | Generate random samples from the posterior predictive distribution of a "GaussianInvWishart" object
rPosteriorPredictive.GaussianNIG | Generate random samples from the posterior predictive distribution of a "GaussianNIG" object
rPosteriorPredictive.GaussianNIW | Generate random samples from the posterior predictive distribution of a "GaussianNIW" object
rPosteriorPredictive.HDP | Generate random samples from the posterior predictive distribution of a "HDP" object
rPosteriorPredictive.HDP2 | Generate random samples from the posterior predictive distribution of a "HDP2" object
rPosteriorPredictive.LinearGaussianGaussian | Generate random samples from the posterior predictive distribution of a "LinearGaussianGaussian" object
rT | Random Generation for (multivariate) t distribution
rWishart | Random generation for Wishart distribution

## -- S --

sufficientStatistics | Get sample sufficient statistics
sufficientStatistics.CatDirichlet | Sufficient statistics of a "CatDirichlet" object
sufficientStatistics.CatDP | Sufficient statistics of a "CatDP" object
sufficientStatistics.DP | Sufficient statistics of a "DP" object
sufficientStatistics.GaussianGaussian | Sufficient statistics of a "GaussianGaussian" object
sufficientStatistics.GaussianInvWishart | Sufficient statistics of a "GaussianInvWishart" object
sufficientStatistics.GaussianNIG | Sufficient statistics of a "GaussianNIG" object
sufficientStatistics.GaussianNIW | Sufficient statistics of a "GaussianNIW" object
sufficientStatistics.HDP | Sufficient statistics of a "HDP" object
sufficientStatistics.HDP2 | Sufficient statistics of a "HDP2" object
sufficientStatistics.LinearGaussianGaussian | Sufficient statistics of a "LinearGaussianGaussian" object
sufficientStatistics_Weighted | Get weighted sample sufficient statistics
sufficientStatistics_Weighted.CatDirichlet | Weighted sufficient statistics of a "CatDirichlet" object
sufficientStatistics_Weighted.CatDP | Weighted sufficient statistics of a "CatDP" object
sufficientStatistics_Weighted.DP | Weighted sufficient statistics of a "DP" object
sufficientStatistics_Weighted.GaussianGaussian | Weighted sufficient statistics of a "GaussianGaussian" object
sufficientStatistics_Weighted.GaussianInvWishart | Weighted sufficient statistics of a "GaussianInvWishart" object
sufficientStatistics_Weighted.GaussianNIG | Weighted sufficient statistics of a "GaussianNIG" object
sufficientStatistics_Weighted.GaussianNIW | Weighted sufficient statistics for a "GaussianNIW" object
sufficientStatistics_Weighted.HDP | Weighted sufficient statistics of a "HDP" object
sufficientStatistics_Weighted.HDP2 | Weighted sufficient statistics of a "HDP2" object
sufficientStatistics_Weighted.LinearGaussianGaussian | Weighted sufficient statistics of a "LinearGaussianGaussian" object

## -- misc --

%plus% | a plus b with NA values