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r-bevimed
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A fast integrative genetic association test for rare diseases based on a model for disease status given allele counts at rare variant sites. Probability of association, mode of inheritance and probability of pathogenicity for individual variants are all inferred in a Bayesian framework - 'A Fast Association Test for Identifying Pathogenic Variants Involved in Rare Diseases', Greene et al 2017 <doi:10.1016/j.ajhg.2017.05.015>.
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2025-04-22 |
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r-betategarch
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Simulation, estimation and forecasting of first-order Beta-Skew-t-EGARCH models with leverage (one-component, two-component, skewed versions).
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2025-04-22 |
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r-bess
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An implementation of best subset selection in generalized linear model and Cox proportional hazard model via the primal dual active set algorithm proposed by Wen, C., Zhang, A., Quan, S. and Wang, X. (2017) <arXiv:1709.06254>. The algorithm formulates coefficient parameters and residuals as primal and dual variables and utilizes efficient active set selection strategies based on the complementarity of the primal and dual variables.
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2025-04-22 |
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r-benfordtests
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Several specialized statistical tests and support functions for determining if numerical data could conform to Benford's law.
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2025-04-22 |
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r-benchr
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Provides infrastructure to accurately measure and compare the execution time of R expressions.
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2025-04-22 |
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r-belg
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Calculates the Boltzmann entropy of a landscape gradient. This package uses the analytical method created by Gao, P., Zhang, H. and Li, Z., 2018 (<doi:10.1111/tgis.12315>). It also extend the original idea by allowing calculations on data with missing values.
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2025-04-22 |
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r-bdgraph
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Statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Mohammadi and Wit (2019) <doi:10.18637/jss.v089.i03>.
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2025-04-22 |
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r-bda
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Functions for density estimation based on grouped data, and next-generation gene expression data.
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2025-04-22 |
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r-bcv
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Methods for choosing the rank of an SVD approximation via cross validation. The package provides both Gabriel-style "block" holdouts and Wold-style "speckled" holdouts. It also includes an implementation of the SVDImpute algorithm. For more information about Bi-cross-validation, see Owen & Perry's 2009 AoAS article (at http://arxiv.org/abs/0908.2062) and Perry's 2009 PhD thesis (at http://arxiv.org/abs/0909.3052).
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2025-04-22 |
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r-bcrypt
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Bindings to the 'blowfish' password hashing algorithm derived from the 'OpenBSD' implementation.
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2025-04-22 |
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r-bcpa
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The Behavioral Change Point Analysis (BCPA) is a method of identifying hidden shifts in the underlying parameters of a time series, developed specifically to be applied to animal movement data which is irregularly sampled. The method is based on: E. Gurarie, R. Andrews and K. Laidre A novel method for identifying behavioural changes in animal movement data (2009) Ecology Letters 12:5 395-408.
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2025-04-22 |
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r-bclust
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Builds a dendrogram using log posterior as a natural distance defined by the model and meanwhile waits the clustering variables. It is also capable to computing equivalent Bayesian discrimination probabilities. The adopted method suites small sample large dimension setting. The model parameter estimation maybe difficult, depending on data structure and the chosen distribution family.
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2025-04-22 |
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r-bcf
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Causal inference for a binary treatment and continuous outcome using Bayesian Causal Forests. See Hahn, Murray and Carvalho (2017) <arXiv:1706.09523> for additional information. This implementation relies on code originally accompanying Pratola et. al. (2013) <arXiv:1309.1906>.
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2025-04-22 |
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r-bcbcsf
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Fully Bayesian Classification with a subset of high-dimensional features, such as expression levels of genes. The data are modeled with a hierarchical Bayesian models using heavy-tailed t distributions as priors. When a large number of features are available, one may like to select only a subset of features to use, typically those features strongly correlated with the response in training cases. Such a feature selection procedure is however invalid since the relationship between the response and the features has be exaggerated by feature selection. This package provides a way to avoid this bias and yield better-calibrated predictions for future cases when one uses F-statistic to select features.
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2025-04-22 |
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r-bbmisc
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Miscellaneous helper functions for and from B. Bischl and some other guys, mainly for package development.
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2025-04-22 |
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r-bayesxsrc
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BayesX performs Bayesian inference in structured additive regression (STAR) models. The R package BayesXsrc provides the BayesX command line tool for easy installation. A convenient R interface is provided in package R2BayesX.
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2025-04-22 |
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r-bayesvarsel
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Conceived to calculate Bayes factors in linear models and then to provide a formal Bayesian answer to testing and variable selection problems. From a theoretical side, the emphasis in this package is placed on the prior distributions and it allows a wide range of them: Jeffreys (1961); Zellner and Siow(1980)<DOI:10.1007/bf02888369>; Zellner and Siow(1984); Zellner (1986)<DOI:10.2307/2233941>; Fernandez et al. (2001)<DOI:10.1016/s0304-4076(00)00076-2>; Liang et al. (2008)<DOI:10.1198/016214507000001337> and Bayarri et al. (2012)<DOI:10.1214/12-aos1013>. The interaction with the package is through a friendly interface that syntactically mimics the well-known lm() command of R. The resulting objects can be easily explored providing the user very valuable information (like marginal, joint and conditional inclusion probabilities of potential variables; the highest posterior probability model, HPM; the median probability model, MPM) about the structure of the true -data generating- model. Additionally, this package incorporates abilities to handle problems with a large number of potential explanatory variables through parallel and heuristic versions of the main commands, Garcia-Donato and Martinez-Beneito (2013)<DOI:10.1080/01621459.2012.742443>.
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2025-04-22 |
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r-bayestree
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This is an implementation of BART:Bayesian Additive Regression Trees, by Chipman, George, McCulloch (2010).
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2025-04-22 |
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r-bayessae
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Provides a variety of methods from Rao (2003, ISBN:0-471-41374-7) and some other research articles to deal with several specific small area area- level models in Bayesian framework. Models provided range from the basic Fay-Herriot model to its improvement such as You-Chapman models, unmatched models, spatial models and so on. Different types of priors for specific parameters could be chosen to obtain MCMC posterior draws. The main sampling function is written in C with GSL lab so as to facilitate the computation. Model internal checking and model comparison criteria are also involved.
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2025-04-22 |
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r-bayesqr
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Bayesian quantile regression using the asymmetric Laplace distribution, both continuous as well as binary dependent variables are supported. The package consists of implementations of the methods of Yu & Moyeed (2001) <doi:10.1016/S0167-7152(01)00124-9>, Benoit & Van den Poel (2012) <doi:10.1002/jae.1216> and Al-Hamzawi, Yu & Benoit (2012) <doi:10.1177/1471082X1101200304>. To speed up the calculations, the Markov Chain Monte Carlo core of all algorithms is programmed in Fortran and called from R.
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2025-04-22 |
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r-bayesm
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Covers many important models used in marketing and micro-econometrics applications. The package includes: Bayes Regression (univariate or multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate Mixtures of Normals (including clustering), Dirichlet Process Prior Density Estimation with normal base, Hierarchical Linear Models with normal prior and covariates, Hierarchical Linear Models with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a mixture of normals prior and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates, Hierarchical Negative Binomial Regression Models, Bayesian analysis of choice-based conjoint data, Bayesian treatment of linear instrumental variables models, Analysis of Multivariate Ordinal survey data with scale usage heterogeneity (as in Rossi et al, JASA (01)), Bayesian Analysis of Aggregate Random Coefficient Logit Models as in BLP (see Jiang, Manchanda, Rossi 2009) For further reference, consult our book, Bayesian Statistics and Marketing by Rossi, Allenby and McCulloch (Wiley 2005) and Bayesian Non- and Semi-Parametric Methods and Applications (Princeton U Press 2014).
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2025-04-22 |
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r-bayesloglin
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The function MC3() searches for log-linear models with the highest posterior probability. The function gibbsSampler() is a blocked Gibbs sampler for sampling from the posterior distribution of the log-linear parameters. The functions findPostMean() and findPostCov() compute the posterior mean and covariance matrix for decomposable models which, for these models, is available in closed form.
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2025-04-22 |
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r-bayesimages
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Various algorithms for segmentation of 2D and 3D images, such as computed tomography and satellite remote sensing. This package implements Bayesian image analysis using the hidden Potts model with external field prior of Moores et al. (2015) <doi:10.1016/j.csda.2014.12.001>. Latent labels are sampled using chequerboard updating or Swendsen-Wang. Algorithms for the smoothing parameter include pseudolikelihood, path sampling, the exchange algorithm, approximate Bayesian computation (ABC-MCMC and ABC-SMC), and the parametric functional approximate Bayesian (PFAB) algorithm. Refer to <doi:10.1007/s11222-014-9525-6> and <doi:10.1214/18-BA1130> for further details.
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2025-04-22 |
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r-aws
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We provide a collection of R-functions implementing adaptive smoothing procedures in 1D, 2D and 3D. This includes the Propagation-Separation Approach to adaptive smoothing as described in "J. Polzehl and V. Spokoiny (2006) <DOI:10.1007/s00440-005-0464-1>", "J. Polzehl and V. Spokoiny (2004) <DOI:10.20347/WIAS.PREPRINT.998>" and "J. Polzehl, K. Papafitsoros, K. Tabelow (2018) <DOI:10.20347/WIAS.PREPRINT.2520>", the Intersecting Confidence Intervals (ICI), variational approaches and a non-local means filter.
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2025-04-22 |
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r-adimpro
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Implements tools for manipulation of digital images and the Propagation Separation approach by Polzehl and Spokoiny (2006) <DOI:10.1007/s00440-005-0464-1> for smoothing digital images, see Polzehl and Tabelow (2007) <DOI:10.18637/jss.v019.i01>.
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2025-04-22 |
