Bayesian Methods and Graphical Model Structures for Statistical Modeling


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Documentation for package ‘bbricks’ version 0.1.4

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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