## model fitting

Functions associated with inference and selection for Bayesian Linear and Generalized Linear Models

BAS

BAS: Bayesian Model Averaging using Bayesian Adaptive Sampling

bas.glm()

Bayesian Adaptive Sampling Without Replacement for Variable Selection in Generalized Linear Models

bas.lm()

Bayesian Adaptive Sampling for Bayesian Model Averaging and Variable Selection in Linear Models

bayesglm.fit()

Fitting Generalized Linear Models and Bayesian marginal likelihood evaluation

coef(<bas>) print(<coef.bas>)

Coefficients of a Bayesian Model Average object

confint(<coef.bas>)

Compute Credible Intervals for BAS regression coefficients from BAS objects

confint(<pred.bas>)

Compute Credible (Bayesian Confidence) Intervals for a BAS predict object

cv.summary.bas()

Summaries for Out of Sample Prediction

diagnostics()

BAS MCMC diagnostic plot

eplogprob()

eplogprob - Compute approximate marginal inclusion probabilities from pvalues

eplogprob.marg()

eplogprob.marg - Compute approximate marginal inclusion probabilities from pvalues

fitted(<bas>)

Fitted values for a BAS BMA objects

force.heredity.bas()

Post processing function to force constraints on interaction inclusion bas BMA objects

image(<bas>)

Images of models used in Bayesian model averaging

plot(<bas>)

Plot Diagnostics for an BAS Object

plot(<coef.bas>)

Plots the posterior distributions of coefficients derived from Bayesian model averaging

plot(<confint.bas>)

Plot Bayesian Confidence Intervals

predict(<bas>)

Prediction Method for an object of class BAS

predict(<basglm>)

Prediction Method for an Object of Class basglm

print(<bas>)

Print a Summary of Bayesian Model Averaging objects from BAS

summary(<bas>)

Summaries of Bayesian Model Averaging objects from BAS

update(<bas>)

Update BAS object using a new prior

variable.names(<pred.bas>)

Extract the variable names for a model from a BAS prediction object

## coefficient priors

beta.prime()

Beta-Prime Prior Distribution for Coefficients in BMA Model

CCH()

Generalized g-Prior Distribution for Coefficients in BMA Models

EB.global()

Find the global Empirical Bayes estimates for BMA

EB.local()

Empirical Bayes Prior Distribution for Coefficients in BMA Model

g.prior()

Families of G-Prior Distribution for Coefficients in BMA Models

hyper.g()

Hyper-g-Prior Distribution for Coefficients in BMA Models

hyper.g.n()

Generalized hyper-g/n Prior Distribution for g for mixtures of g-priors on Coefficients in BMA Models

IC.prior()

Information Criterion Families of Prior Distribution for Coefficients in BMA Models

intrinsic()

Intrinsic Prior Distribution for Coefficients in BMA Models

Jeffreys()

Jeffreys Prior Distribution for $g$ for Mixtures of g-Priors for Coefficients in BMA Models

robust()

Robust-Prior Distribution for Coefficients in BMA Model

tCCH()

Generalized tCCH g-Prior Distribution for Coefficients in BMA Models

TG()

Generalized g-Prior Distribution for Coefficients in BMA Models

testBF.prior()

Test based Bayes Factors for BMA Models

## model priors

Bernoulli()

Independent Bernoulli Prior Distribution for Models

Bernoulli.heredity()

Independent Bernoulli prior on models that with constraints for model hierarchy induced by interactions

beta.binomial()

Beta-Binomial Prior Distribution for Models

tr.beta.binomial()

Truncated Beta-Binomial Prior Distribution for Models

tr.poisson()

Truncated Poisson Prior Distribution for Models

tr.power.prior()

Truncated Power Prior Distribution for Models

uniform()

Uniform Prior Distribution for Models

## special functions

hypergeometric1F1()

Confluent hypergeometric2F1 function

hypergeometric2F1()

Gaussian hypergeometric2F1 function

phi1()

Compound Confluent hypergeometric function of two variables

## utility functions

Bayes.outlier()

Bayesian Outlier Detection

list2matrix.bas()

Coerce a BAS list object into a matrix.

list2matrix.which()

Coerce a BAS list object into a matrix.

which.matrix()

Coerce a BAS list object of models into a matrix.

## data sets

Hald

Hald Data

bodyfat

Bodyfat Data

protein

Protein Activity Data

## all functions

BAS

BAS: Bayesian Model Averaging using Bayesian Adaptive Sampling

Bayes.outlier()

Bayesian Outlier Detection

Bernoulli()

Independent Bernoulli Prior Distribution for Models

Bernoulli.heredity()

Independent Bernoulli prior on models that with constraints for model hierarchy induced by interactions

CCH()

Generalized g-Prior Distribution for Coefficients in BMA Models

EB.global()

Find the global Empirical Bayes estimates for BMA

EB.local()

Empirical Bayes Prior Distribution for Coefficients in BMA Model

Hald

Hald Data

IC.prior()

Information Criterion Families of Prior Distribution for Coefficients in BMA Models

Jeffreys()

Jeffreys Prior Distribution for $g$ for Mixtures of g-Priors for Coefficients in BMA Models

TG()

Generalized g-Prior Distribution for Coefficients in BMA Models

bas.glm()

Bayesian Adaptive Sampling Without Replacement for Variable Selection in Generalized Linear Models

bas.lm()

Bayesian Adaptive Sampling for Bayesian Model Averaging and Variable Selection in Linear Models

bayesglm.fit()

Fitting Generalized Linear Models and Bayesian marginal likelihood evaluation

beta.binomial()

Beta-Binomial Prior Distribution for Models

beta.prime()

Beta-Prime Prior Distribution for Coefficients in BMA Model

bodyfat

Bodyfat Data

climate

Climate Data

coef(<bas>) print(<coef.bas>)

Coefficients of a Bayesian Model Average object

confint(<coef.bas>)

Compute Credible Intervals for BAS regression coefficients from BAS objects

confint(<pred.bas>)

Compute Credible (Bayesian Confidence) Intervals for a BAS predict object

crabs

Horseshoe Crab Data

cv.summary.bas()

Summaries for Out of Sample Prediction

diagnostics()

BAS MCMC diagnostic plot

eplogprob()

eplogprob - Compute approximate marginal inclusion probabilities from pvalues

eplogprob.marg()

eplogprob.marg - Compute approximate marginal inclusion probabilities from pvalues

extract_MPM()

Extract the Median Probability Model

fitted(<bas>)

Fitted values for a BAS BMA objects

force.heredity.bas()

Post processing function to force constraints on interaction inclusion bas BMA objects

g.prior()

Families of G-Prior Distribution for Coefficients in BMA Models

hyper.g()

Hyper-g-Prior Distribution for Coefficients in BMA Models

hyper.g.n()

Generalized hyper-g/n Prior Distribution for g for mixtures of g-priors on Coefficients in BMA Models

hypergeometric1F1()

Confluent hypergeometric2F1 function

hypergeometric2F1()

Gaussian hypergeometric2F1 function

image(<bas>)

Images of models used in Bayesian model averaging

intrinsic()

Intrinsic Prior Distribution for Coefficients in BMA Models

list2matrix.bas()

Coerce a BAS list object into a matrix.

list2matrix.which()

Coerce a BAS list object into a matrix.

phi1()

Compound Confluent hypergeometric function of two variables

plot(<bas>)

Plot Diagnostics for an BAS Object

plot(<coef.bas>)

Plots the posterior distributions of coefficients derived from Bayesian model averaging

plot(<confint.bas>)

Plot Bayesian Confidence Intervals

predict(<bas>)

Prediction Method for an object of class BAS

predict(<basglm>)

Prediction Method for an Object of Class basglm

print(<bas>)

Print a Summary of Bayesian Model Averaging objects from BAS

protein

Protein Activity Data

robust()

Robust-Prior Distribution for Coefficients in BMA Model

summary(<bas>)

Summaries of Bayesian Model Averaging objects from BAS

tCCH()

Generalized tCCH g-Prior Distribution for Coefficients in BMA Models

testBF.prior()

Test based Bayes Factors for BMA Models

tr.beta.binomial()

Truncated Beta-Binomial Prior Distribution for Models

tr.poisson()

Truncated Poisson Prior Distribution for Models

tr.power.prior()

Truncated Power Prior Distribution for Models

uniform()

Uniform Prior Distribution for Models

update(<bas>)

Update BAS object using a new prior

variable.names(<pred.bas>)

Extract the variable names for a model from a BAS prediction object

which.matrix()

Coerce a BAS list object of models into a matrix.