The R package BiDAG implements Markov chain Monte Carlo (MCMC) methods for structure learning and sampling of Bayesian networks. The package includes tools to search for a maximum a posteriori (MAP) graph and to sample graphs from the posterior distribution given the data. A new hybrid approach to structure learning enables inference in large graphs. In the first step, we define a reduced search space by means of the PC algorithm or based on prior knowledge. In the second step, an iterative order MCMC scheme proceeds to optimize within the restricted search space and estimate the MAP graph. Sampling from the posterior distribution is implemented using either order or partition MCMC. The models and algorithms can handle both discrete and continuous data. The BiDAG package also provides an implementation of MCMC schemes for structure learning and sampling of dynamic Bayesian networks.
The aghq package for implementing approximate Bayesian inference using adaptive quadrature is introduced. The method and software are described, and use of the package in making approximate Bayesian inferences in several challenging low- and high-dimensional models is illustrated. Examples include an infectious disease model; an astrostatistical model for estimating the mass of the Milky Way; two examples in non-Gaussian model-based geostatistics including one incorporating zero-inflation which is not easily fit using other methods; and a model for zero-inflated, overdispersed count data. The …
The INLA package provides a tool for computationally efficient Bayesian modeling and inference for various widely used models, more formally the class of latent Gaussian models. It is a non-sampling based framework which provides approximate results for Bayesian inference, using sparse matrices. The swift uptake of this framework for Bayesian modeling is rooted in the computational efficiency of the approach and catalyzed by the demand presented by the big data era. In this paper, we present new developments within the INLA package with the aim to provide a computationally efficient mechanism …
Bayesian penalized regression techniques, such as the Bayesian lasso and the Bayesian horseshoe estimator, have recently received a significant amount of attention in the statistics literature. However, software implementing state-of-the-art Bayesian penalized regression, outside of general purpose Markov chain Monte Carlo platforms such as STAN, is relatively rare. This paper introduces bayesreg, a new toolbox for fitting Bayesian penalized regression models with continuous shrinkage prior densities. The toolbox features Bayesian linear regression with Gaussian or heavy-tailed error models an…
For log-linear analysis, the hyper Dirichlet conjugate prior is available to work in the Bayesian paradigm. With this prior, the MC3 algorithm allows for exploration of the space of models to try to find those with the highest posterior probability. Once top models have been identified, a block Gibbs sampler can be constructed to sample from the posterior distribution and to estimate parameters of interest. Our aim in this paper, is to introduce the bayesloglin R package \citep{R} which contains functions to carry out these tasks.
We present the BayesBD package providing Bayesian inference for boundaries of noisy images. The BayesBD package implements flexible Gaussian process priors indexed by the circle to recover the boundary in a binary or Gaussian noised image, with the benefits of guaranteed geometric restrictions on the estimated boundary, (nearly) minimax optimal and smoothness adaptive convergence rates, and convenient joint inferences under certain assumptions. The core sampling tasks for our model have linear complexity, and our implementation in c++ using packages Rcpp and RcppArmadillo is computationally ef…
Bayesian synthetic likelihood (BSL) is a popular method for estimating the parameter posterior distribution for complex statistical models and stochastic processes that possess a computationally intractable likelihood function. Instead of evaluating the likelihood, BSL approximates the likelihood of a judiciously chosen summary statistic of the data via model simulation and density estimation. Compared to alternative methods such as approximate Bayesian computation (ABC), BSL requires little tuning and requires less model simulations than ABC when the chosen summary statistic is high-dimension…
The random-effects or normal-normal hierarchical model is commonly utilized in a wide range of meta-analysis applications. A Bayesian approach to inference is very attractive in this context, especially when a meta-analysis is based only on few studies. The bayesmeta R package provides readily accessible tools to perform Bayesian meta-analyses and generate plots and summaries, without having to worry about computational details. It allows for flexible prior specification and instant access to the resulting posterior distributions, including prediction and shrinkage estimation, and facilitating…
Learning graphical models from data is an important problem with wide applications, ranging from genomics to the social sciences. Nowadays datasets often have upwards of thousands---sometimes tens or hundreds of thousands---of variables and far fewer samples. To meet this challenge, we have developed a new R package called sparsebn for learning the structure of large, sparse graphical models with a focus on Bayesian networks. While there are many existing software packages for this task, this package focuses on the unique setting of learning large networks from high-dimensional data, possibly …
varstan is an \proglang{R} package for Bayesian analysis of time series models using \proglang{Stan}. The package offers a dynamic way to choose a model, define priors in a wide range of distributions, check model's fit, and forecast with the m-steps ahead predictive distribution. The users can widely choose between implemented models such as \textit{multiplicative seasonal ARIMA, dynamic regression, random walks, GARCH, dynamic harmonic regressions,VARMA, stochastic Volatility Models, and generalized t-student with unknown degree freedom GARCH models}. Every model constructor in \pkg{varstan}…
In this article, we present a recently released R package for Bayesian calibration. Many industrial fields are facing unfeasible or costly field experiments. These experiments are replaced with numerical/computer experiments which are realized by running a numerical code. Bayesian calibration intends to estimate, through a posterior distribution, input parameters of the code in order to make the code outputs close to the available experimental data. The code can be time consuming while the Bayesian calibration implies a lot of code calls which makes studies too burdensome. A discrepancy might …
Bayesian additive regression tree (BART) models have seen increased attention in recent years as a general-purpose nonparametric modeling technique. BART combines the flexibility of modern machine learning techniques with the principled uncertainty quantification of Bayesian inference, and it has been shown to be uniquely appropriate for addressing the high-noise problems that occur commonly in many areas of science, including medicine and the social sciences. This paper introduces the SoftBart package for fitting the Soft BART algorithm of Linero and Yang (2018). In addition to improving upon…
The Bergm package provides a comprehensive framework for Bayesian inference using Markov chain Monte Carlo (MCMC) algorithms. It can also supply graphical Bayesian goodness-of-fit procedures that address the issue of model adequacy. The package is simple to use and represents an attractive way of analysing network data as it offers the advantage of a complete probabilistic treatment of uncertainty. Bergm is based on the ergm package and therefore it makes use of the same model set-up and network simulation algorithms. The Bergm package has been continually improved in terms of speed performanc…
In this paper we briefly review the main methodological aspects concerned with the application of the Bayesian approach to model choice and model averaging in the context of variable selection in regression models. This includes prior elicitation, summaries of the posterior distribution and computational strategies. We then examine and compare various publicly available {\tt R}-packages for its practical implementation summarizing and explaining the differences between packages and giving recommendations for applied users. We find that all packages reviewed lead to very similar results, but th…
This paper describes and illustrates new functionality for fitting spatially varying coefficients models in the spBayes (version 0.4-2) R package. The new spSVC function uses a computationally efficient Markov chain Monte Carlo algorithm and extends current spBayes functions, that fit only space-varying intercept regression models, to fit independent or multivariate Gaussian process random effects for any set of columns in the regression design matrix. Newly added OpenMP parallelization options for spSVC are discussed and illustrated, as well as helper functions for joint and point-wise predic…
Recent developments in data science and big data research have produced an abundance of large data sets that are too big to be analyzed in their entirety, due to limits on either computer memory or storage capacity. Here, we introduce our R package 'BayesSummaryStatLM' for Bayesian linear regression models with Markov chain Monte Carlo implementation that overcomes these limitations. Our Bayesian models use only summary statistics of data as input; these summary statistics can be calculated from subsets of big data and combined over subsets. Thus, complete data sets do not need to be read into…
The brms package allows R users to easily specify a wide range of Bayesian single-level and multilevel models, which are fitted with the probabilistic programming language Stan behind the scenes. Several response distributions are supported, of which all parameters (e.g., location, scale, and shape) can be predicted at the same time thus allowing for distributional regression. Non-linear relationships may be specified using non-linear predictor terms or semi-parametric approaches such as splines or Gaussian processes. To make all of these modeling options possible in a multilevel framework, br…
We describe the R package acebayes and demonstrate its use to find Bayesian optimal experimental designs. A decision-theoretic approach is adopted, with the optimal design maximising an expected utility. Finding Bayesian optimal designs for realistic problems is challenging, as the expected utility is typically intractable and the design space may be high-dimensional. The package implements the approximate coordinate exchange algorithm to optimise (an approximation to) the expected utility via a sequence of conditional one-dimensional optimisation steps. At each step, a Gaussian process regres…
Hypothesis testing is a central statistical method in psychology and the cognitive sciences. However, the problems of null hypothesis significance testing (NHST) and p-values have been debated widely, but few attractive alternatives exist. This article introduces the fbst R package, which implements the Full Bayesian Significance Test (FBST) to test a sharp null hypothesis against its alternative via the e-value. The statistical theory of the FBST has been introduced by Pereira et al. (1999) more than two decades ago and since then, the FBST has shown to be a Bayesian alternative to NHST and p…
A fast, flexible simulation framework for Bayesian adaptive designs -- the R package BATSS
MRC Biostatistics Unit, University of Cambridge（剑桥大学医学研究委员会生物统计学单位）；School of Public Health and Preventive Medicine, Monash University（莫纳什大学公共卫生与预防医学院）；Faculty of Informatics and Data Science, University of Regensburg（雷根斯堡大学信息科学与数据科学学院）
BayesMallows is an R package for analyzing data in the form of rankings or preferences with the Mallows rank model, and its finite mixture extension, in a Bayesian probabilistic framework. The Mallows model is a well-known model, grounded on the idea that the probability density of an observed ranking decreases exponentially fast as its distance to the location parameter increases. Despite the model being quite popular, this is the first Bayesian implementation that allows a wide choice of distances, and that works well with a large amount of items to be ranked. BayesMallows supports footrule,…
The INLAMSM package for the R programming language provides a collection of multivariate spatial models for lattice data that can be used with package INLA for Bayesian inference. The multivariate spatial models include different structures to model the spatial variation of the variables and the between-variables variability. In this way, fitting multivariate spatial models becomes faster and easier. The use of the different models included in the package is illustrated using two different datasets: the well-known North Carolina SIDS data and mortality by three causes of death in Comunidad Val…
Synthetic data is a promising approach to privacy protection in many contexts. A Bayesian synthesis model, also known as a synthesizer, simulates synthetic values of sensitive variables from their posterior predictive distributions. The resulting synthetic data can then be released in place of the confidential data. An important evaluation prior to synthetic data release is its level of privacy protection, which is often in the form of disclosure risks evaluation. Attribute disclosure, referring to an intruder correctly inferring the confidential values of synthetic records, is one type of dis…
This article introduces epidemia, an R package for Bayesian, regression-oriented modeling of infectious diseases. The implemented models define a likelihood for all observed data while also explicitly modeling transmission dynamics: an approach often termed as semi-mechanistic. Infections are propagated over time using renewal equations. This approach is inspired by self-exciting, continuous-time point processes such as the Hawkes process. A variety of inferential tasks can be performed using the package. Key epidemiological quantities, including reproduction numbers and latent infections, may…
The CompModels package for R provides a suite of computer model test functions that can be used for computer model prediction/emulation, uncertainty quantification, and calibration, but in particular, the sequential optimization of computer models. The package is a mix of real-world physics problems, known mathematical functions, and black-box functions that have been converted into computer models with the goal of Bayesian (i.e., sequential) optimization in mind. Likewise, the package contains computer models that represent either the constrained or unconstrained optimization case, each with …
Compared to abundant classical statistics-based literature, to date, very little Bayesian literature exists on Procrustes shape analysis in Geometric Morphometrics, probably because of being a relatively new branch of statistical research and because of inherent computational difficulty associated with Bayesian analysis. Moreover, we may obtain a plethora of novel inferences from Bayesian Procrustes analysis of shape parameter distributions. In this paper, we propose to regard the posterior of Procrustes shape variance as morphological variability indicators. Here we propose novel Bayesian met…
Leibniz University Hannover（莱布尼茨汉诺威大学）；University of Freiburg（弗莱堡大学）；Bosch Center for Artificial Intelligence（博世人工智能中心）
Algorithm parameters, in particular hyperparameters of machine learning algorithms, can substantially impact their performance. To support users in determining well-performing hyperparameter configurations for their algorithms, datasets and applications at hand, SMAC3 offers a robust and flexible framework for Bayesian Optimization, which can improve performance within a few evaluations. It offers several facades and pre-sets for typical use cases, such as optimizing hyperparameters, solving low dimensional continuous (artificial) global optimization problems and configuring algorithms to perf…
Most of applied statistics involves regression analysis of data. This paper presents a stand-alone and menu-driven software package, Bayesian Regression: Nonparametric and Parametric Models. Currently, this package gives the user a choice from 83 Bayesian models for data analysis. They include 47 Bayesian nonparametric (BNP) infinite-mixture regression models; 5 BNP infinite-mixture models for density estimation; and 31 normal random effects models (HLMs), including normal linear models. Each of the 78 regression models handles either a continuous, binary, or ordinal dependent variable, and ca…
This article introduces the bpcs R package (Bayesian Paired Comparison in Stan) and the statistical models implemented in the package. This package aims to facilitate the use of Bayesian models for paired comparison data in behavioral research. Bayesian analysis of paired comparison data allows parameter estimation even in conditions where the maximum likelihood does not exist, allows easy extension of paired comparison models, provide straightforward interpretation of the results with credible intervals, have better control of type I error, have more robust evidence towards the null hypothesi…
The R package BNSP provides a unified framework for semiparametric location-scale regression and stochastic search variable selection. The statistical methodology that the package is built upon utilizes basis function expansions to represent semiparametric covariate effects in the mean and variance functions, and spike-slab priors to perform selection and regularization of the estimated effects. In addition to the main function that performs posterior sampling, the package includes functions for assessing convergence of the sampler, summarizing model fits, visualizing covariate effects and obt…
We present dynesty, a public, open-source, Python package to estimate Bayesian posteriors and evidences (marginal likelihoods) using Dynamic Nested Sampling. By adaptively allocating samples based on posterior structure, Dynamic Nested Sampling has the benefits of Markov Chain Monte Carlo algorithms that focus exclusively on posterior estimation while retaining Nested Sampling's ability to estimate evidences and sample from complex, multi-modal distributions. We provide an overview of Nested Sampling, its extension to Dynamic Nested Sampling, the algorithmic challenges involved, and the variou…
In this paper we describe the main featuress of the Bergm package for the open-source R software which provides a comprehensive framework for Bayesian analysis for exponential random graph models: tools for parameter estimation, model selection and goodness-of-fit diagnostics. We illustrate the capabilities of this package describing the algorithms through a tutorial analysis of two well-known network datasets.
Università Cattolica del Sacro Cuore（天主教圣心大学）；Università degli Studi di Milano-Bicocca（米兰比可卡大学）
Directed Acyclic Graphs (DAGs) provide a powerful framework to model causal relationships among variables in multivariate settings; in addition, through the do-calculus theory, they allow for the identification and estimation of causal effects between variables also from pure observational data. In this setting, the process of inferring the DAG structure from the data is referred to as causal structure learning or causal discovery. We introduce BCDAG, an R package for Bayesian causal discovery and causal effect estimation from Gaussian observational data, implementing the Markov chain Monte Ca…
Recent advances in big data and analytics research have provided a wealth of large data sets that are too big to be analyzed in their entirety, due to restrictions on computer memory or storage size. New Bayesian methods have been developed for large data sets that are only large due to large sample sizes; these methods partition big data sets into subsets, and perform independent Bayesian Markov chain Monte Carlo analyses on the subsets. The methods then combine the independent subset posterior samples to estimate a posterior density given the full data set. These approaches were shown to be …
Recent technological advances have provided new settings to enhance individual-based data collection and computerized-tracking data have became common in many behavioral and social research. By adopting instantaneous tracking devices such as computer-mouse, wii, and joysticks, such data provide new insights for analysing the dynamic unfolding of response process. ssMousetrack is a R package for modeling and analysing computerized-tracking data by means of a Bayesian state-space approach. The package provides a set of functions to prepare data, fit the model, and assess results via simple diagn…
This is a vignette for the R package eggCounts version 2.0. The package implements a suite of Bayesian hierarchical models dealing with faecal egg count reductions. The models are designed for a variety of practical situations, including individual treatment efficacy, zero inflation, small sample size (less than 10) and potential outliers. The functions are intuitive to use and their output are easy to interpret, such that users are protected from being exposed to complex Bayesian hierarchical modelling tasks. In addition, the package includes plotting functions to display data and results in …
We present a new package in R implementing Bayesian additive regression trees (BART). The package introduces many new features for data analysis using BART such as variable selection, interaction detection, model diagnostic plots, incorporation of missing data and the ability to save trees for future prediction. It is significantly faster than the current R implementation, parallelized, and capable of handling both large sample sizes and high-dimensional data.
BayesPy is an open-source Python software package for performing variational Bayesian inference. It is based on the variational message passing framework and supports conjugate exponential family models. By removing the tedious task of implementing the variational Bayesian update equations, the user can construct models faster and in a less error-prone way. Simple syntax, flexible model construction and efficient inference make BayesPy suitable for both average and expert Bayesian users. It also supports some advanced methods such as stochastic and collapsed variational inference.
We present SPUX - a modular framework for Bayesian inference enabling uncertainty quantification and propagation in linear and nonlinear, deterministic and stochastic models, and supporting Bayesian model selection. SPUX can be coupled to any serial or parallel application written in any programming language, (e.g. including Python, R, Julia, C/C++, Fortran, Java, or a binary executable), scales effortlessly from serial runs on a personal computer to parallel high performance computing clusters, and aims to provide a platform particularly suited to support and foster reproducibility in computa…
BPEC is an R package for Bayesian Phylogeographic and Ecological Clustering which allows geographical, environmental and phenotypic measurements to be combined with DNA sequences in order to reveal clustered structure resulting from migration events. DNA sequences are modelled using a collapsed version of a simplified coalescent model projected onto haplotype trees, which subsequently give rise to constrained clusterings as migrations occur. Within each cluster, a multivariate Gaussian distribution of the covariates (geographical, environmental, phenotypic) is used. Inference follows tailored …
The INLA approach for approximate Bayesian inference for latent Gaussian models has been shown to give fast and accurate estimates of posterior marginals and also to be a valuable tool in practice via the R-package R-INLA. In this paper we formalize new developments in the R-INLA package and show how these features greatly extend the scope of models that can be analyzed by this interface. We also discuss the current default method in R-INLA to approximate posterior marginals of the hyperparameters using only a modest number of evaluations of the joint posterior distribution of the hyperparamet…
University of Oxford（牛津大学）；Northeastern University（东北大学）
We present the first general purpose framework for marginal maximum a posteriori estimation of probabilistic program variables. By using a series of code transformations, the evidence of any probabilistic program, and therefore of any graphical model, can be optimized with respect to an arbitrary subset of its sampled variables. To carry out this optimization, we develop the first Bayesian optimization package to directly exploit the source code of its target, leading to innovations in problem-independent hyperpriors, unbounded optimization, and implicit constraint satisfaction; delivering sig…
Generalized additive models (GAMs) are flexible non-linear regression models, which can be fitted efficiently using the approximate Bayesian methods provided by the mgcv R package. While the GAM methods provided by mgcv are based on the assumption that the response distribution is modelled parametrically, here we discuss more flexible methods that do not entail any parametric assumption. In particular, this article introduces the qgam package, which is an extension of mgcv providing fast calibrated Bayesian methods for fitting quantile GAMs (QGAMs) in R. QGAMs are based on a smooth version of …
This paper introduces the \proglang{R} package \pkg{meta4diag} for implementing Bayesian bivariate meta-analyses of diagnostic test studies. Our package \pkg{meta4diag} is a purpose-built front end of the \proglang{R} package \pkg{INLA}. While \pkg{INLA} offers full Bayesian inference for the large set of latent Gaussian models using integrated nested Laplace approximations, \pkg{meta4diag} extracts the features needed for bivariate meta-analysis and presents them in an intuitive way. It allows the user a straightforward model-specification and offers user-specific prior distributions. Further…
The identification of groups' prototypes, i.e. elements of a dataset that represent different groups of data points, may be relevant to the tasks of clustering, classification and mixture modeling. The R package pivmet presented in this paper includes different methods for extracting pivotal units from a dataset. One of the main applications of pivotal methods is a Markov Chain Monte Carlo (MCMC) relabelling procedure to solve the label switching in Bayesian estimation of mixture models. Each method returns posterior estimates, and a set of graphical tools for visualizing the output. The packa…
Motivation: NMR spectra are widely used in metabolomics to obtain metabolite profiles in complex biological mixtures. Common methods used to assign and estimate concentrations of metabolites involve either an expert manual peak fitting or extra pre-processing steps, such as peak alignment and binning. Peak fitting is very time consuming and is subject to human error. Conversely, alignment and binning can introduce artefacts and limit immediate biological interpretation of models. Results: We present the Bayesian AuTomated Metabolite Analyser for NMR spectra (BATMAN), an R package which deconvo…
