# BAS v1.5.5

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## Bayesian Variable Selection and Model Averaging using Bayesian Adaptive Sampling

Package for Bayesian Variable Selection and Model Averaging
in linear models and generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
mixture of g-priors from Liang et al (2008)
<DOI:10.1198/016214507000001337>
for linear models or mixtures of g-priors from Li and Clyde
(2019) <DOI:10.1080/01621459.2018.1469992> in generalized linear models.
Other model selection criteria include AIC, BIC and Empirical Bayes
estimates of g. Sampling probabilities may be updated based on the sampled
models using sampling w/out replacement or an efficient MCMC algorithm which
samples models using a tree structure of the model space
as an efficient hash table. See Clyde, Ghosh and Littman (2010)
<DOI:10.1198/jcgs.2010.09049> for details on the sampling algorithms.
Uniform priors over all models or beta-binomial prior distributions on
model size are allowed, and for large p truncated priors on the model
space may be used to enforce sampling models that are full rank.
The user may force variables to always be included in addition to imposing
constraints that higher order interactions are included only if their
parents are included in the model.
This material is based upon work supported by the National Science
Foundation under Division of Mathematical Sciences grant 1106891.
Any opinions, findings, and
conclusions or recommendations expressed in this material are those of
the author(s) and do not necessarily reflect the views of the
National Science Foundation.

## Functions in BAS

Name | Description | |

TG | Generalized g-Prior Distribution for Coefficients in BMA Models | |

bodyfat | Bodyfat Data | |

climate | Climate Data | |

g.prior | Families of G-Prior Distribution for Coefficients in BMA Models | |

bayesglm.fit | Fitting Generalized Linear Models and Bayesian marginal likelihood evaluation | |

bas.lm | Bayesian Adaptive Sampling for Bayesian Model Averaging and Variable Selection in Linear Models | |

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

eplogprob | eplogprob - Compute approximate marginal inclusion probabilities from pvalues | |

diagnostics | BAS MCMC diagnostic plot | |

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

hyper.g | Hyper-g-Prior Distribution for Coefficients in BMA Models | |

Bayes.outlier | Bayesian Outlier Detection | |

bas.glm | Bayesian Adaptive Sampling Without Replacement for Variable Selection in Generalized Linear Models | |

confint.coef.bas | Compute Credible Intervals for BAS regression coefficients from BAS objects | |

testBF.prior | Test based Bayes Factors for BMA Models | |

tCCH | Generalized tCCH g-Prior Distribution for Coefficients in BMA Models | |

plot.coef.bas | Plots the posterior distributions of coefficients derived from Bayesian model averaging | |

hypergeometric1F1 | Confluent hypergeometric2F1 function | |

intrinsic | Intrinsic Prior Distribution for Coefficients in BMA Models | |

image.bas | Images of models used in Bayesian model averaging | |

coef.bas | Coefficients of a Bayesian Model Average object | |

hypergeometric2F1 | Gaussian hypergeometric2F1 function | |

protein | Protein Activity Data | |

variable.names.pred.bas | Extract the variable names for a model from a BAS prediction object | |

eplogprob.marg | eplogprob.marg - Compute approximate marginal inclusion probabilities from pvalues | |

which.matrix | Coerce a BAS list object of models into a matrix. | |

predict.bas | Prediction Method for an object of class BAS | |

update.bas | Update BAS object using a new prior | |

print.bas | Print a Summary of Bayesian Model Averaging objects from BAS | |

plot.confint.bas | Plot Bayesian Confidence Intervals | |

predict.basglm | Prediction Method for an Object of Class basglm | |

fitted.bas | Fitted values for a BAS BMA objects | |

beta.binomial | Beta-Binomial Prior Distribution for Models | |

beta.prime | Beta-Prime Prior Distribution for Coefficients in BMA Model | |

phi1 | Compound Confluent hypergeometric function of two variables | |

plot.bas | Plot Diagnostics for an BAS Object | |

list2matrix.bas | Coerce a BAS list object into a matrix. | |

cv.summary.bas | Summaries for Out of Sample Prediction | |

list2matrix.which | Coerce a BAS list object into a matrix. | |

confint.pred.bas | Compute Credible (Bayesian Confidence) Intervals for a BAS predict object | |

uniform | Uniform Prior Distribution for Models | |

tr.poisson | Truncated Poisson Prior Distribution for Models | |

tr.power.prior | Truncated Power Prior Distribution for Models | |

tr.beta.binomial | Truncated Beta-Binomial Prior Distribution for Models | |

robust | Robust-Prior Distribution for Coefficients in BMA Model | |

summary.bas | Summaries of Bayesian Model Averaging objects from BAS | |

CCH | Generalized g-Prior Distribution for Coefficients in BMA Models | |

EB.global | Find the global Empirical Bayes estimates for BMA | |

BAS | BAS: Bayesian Model Averaging using Bayesian Adaptive Sampling | |

Bernoulli | Independent Bernoulli Prior Distribution for Models | |

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

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 | |

EB.local | Empirical Bayes Prior Distribution for Coefficients in BMA Model | |

Hald | Hald Data | |

No Results! |

## Vignettes of BAS

Name | ||

BAS-vignette.Rmd | ||

No Results! |

## Last month downloads

## Details

Date | 2020-1-24 |

License | GPL (>= 3) |

URL | https://www.r-project.org, https://github.com/merliseclyde/BAS |

BugReports | https://github.com/merliseclyde/BAS/issues |

Repository | CRAN |

NeedsCompilation | yes |

ByteCompile | yes |

VignetteBuilder | knitr |

Encoding | UTF-8 |

RoxygenNote | 7.0.2 |

Packaged | 2020-01-24 21:57:29 UTC; mclyde |

Date/Publication | 2020-01-24 22:50:14 UTC |

suggests | covr , dplyr , GGally , ggplot2 , glmbb , knitr , MASS , pkgdown , rmarkdown , roxygen2 , testthat |

imports | graphics , grDevices , stats , utils |

depends | R (>= 3.0) |

Contributors | Michael Littman, Joyee Ghosh, Quanli Wang, Yingbo Li, Don van de Bergh |

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