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Showing 11 of total 11 results (show query)

paul-buerkner

brms:Bayesian Regression Models using 'Stan'

Fit Bayesian generalized (non-)linear multivariate multilevel models using 'Stan' for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include both theory-driven and data-driven non-linear terms, auto-correlation structures, censoring and truncation, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their prior knowledge. Models can easily be evaluated and compared using several methods assessing posterior or prior predictions. References: Bürkner (2017) <doi:10.18637/jss.v080.i01>; Bürkner (2018) <doi:10.32614/RJ-2018-017>; Bürkner (2021) <doi:10.18637/jss.v100.i05>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.

Maintained by Paul-Christian Bürkner. Last updated 4 days ago.

bayesian-inference brms multilevel-models stan statistical-models

1.3k stars 16.64 score 13k scripts 35 dependents

stan-dev

posterior:Tools for Working with Posterior Distributions

Provides useful tools for both users and developers of packages for fitting Bayesian models or working with output from Bayesian models. The primary goals of the package are to: (a) Efficiently convert between many different useful formats of draws (samples) from posterior or prior distributions. (b) Provide consistent methods for operations commonly performed on draws, for example, subsetting, binding, or mutating draws. (c) Provide various summaries of draws in convenient formats. (d) Provide lightweight implementations of state of the art posterior inference diagnostics. References: Vehtari et al. (2021) <doi:10.1214/20-BA1221>.

Maintained by Paul-Christian Bürkner. Last updated 2 days ago.

bayes bayesian mcmc

168 stars 16.21 score 3.3k scripts 346 dependents

stan-dev

rstanarm:Bayesian Applied Regression Modeling via Stan

Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.

Maintained by Ben Goodrich. Last updated 11 days ago.

bayesian bayesian-data-analysis bayesian-inference bayesian-methods bayesian-statistics multilevel-models rstan rstanarm stan statistical-modeling cpp

393 stars 15.70 score 5.0k scripts 13 dependents

stan-dev

cmdstanr:R Interface to 'CmdStan'

A lightweight interface to 'Stan' <https://mc-stan.org>. The 'CmdStanR' interface is an alternative to 'RStan' that calls the command line interface for compilation and running algorithms instead of interfacing with C++ via 'Rcpp'. This has many benefits including always being compatible with the latest version of Stan, fewer installation errors, fewer unexpected crashes in RStudio, and a more permissive license.

Maintained by Andrew Johnson. Last updated 8 hours ago.

bayes bayesian markov-chain-monte-carlo maximum-likelihood mcmc stan variational-inference

145 stars 12.65 score 5.2k scripts 9 dependents

nicholasjclark

mvgam:Multivariate (Dynamic) Generalized Additive Models

Fit Bayesian Dynamic Generalized Additive Models to multivariate observations. Users can build nonlinear State-Space models that can incorporate semiparametric effects in observation and process components, using a wide range of observation families. Estimation is performed using Markov Chain Monte Carlo with Hamiltonian Monte Carlo in the software 'Stan'. References: Clark & Wells (2023) <doi:10.1111/2041-210X.13974>.

Maintained by Nicholas J Clark. Last updated 16 hours ago.

bayesian-statistics dynamic-factor-models ecological-modelling forecasting gaussian-process generalised-additive-models generalized-additive-models joint-species-distribution-modelling multilevel-models multivariate-timeseries stan time-series-analysis timeseries vector-autoregression vectorautoregression cpp

148 stars 9.92 score 117 scripts

ropensci

dynamite:Bayesian Modeling and Causal Inference for Multivariate Longitudinal Data

Easy-to-use and efficient interface for Bayesian inference of complex panel (time series) data using dynamic multivariate panel models by Helske and Tikka (2024) <doi:10.1016/j.alcr.2024.100617>. The package supports joint modeling of multiple measurements per individual, time-varying and time-invariant effects, and a wide range of discrete and continuous distributions. Estimation of these dynamic multivariate panel models is carried out via 'Stan'. For an in-depth tutorial of the package, see (Tikka and Helske, 2024) <doi:10.48550/arXiv.2302.01607>.

Maintained by Santtu Tikka. Last updated 4 days ago.

bayesian-inference panel-data stan statistical-models

29 stars 7.90 score 20 scripts

wjakethompson

measr:Bayesian Psychometric Measurement Using 'Stan'

Estimate diagnostic classification models (also called cognitive diagnostic models) with 'Stan'. Diagnostic classification models are confirmatory latent class models, as described by Rupp et al. (2010, ISBN: 978-1-60623-527-0). Automatically generate 'Stan' code for the general loglinear cognitive diagnostic diagnostic model proposed by Henson et al. (2009) <doi:10.1007/s11336-008-9089-5> and other subtypes that introduce additional model constraints. Using the generated 'Stan' code, estimate the model evaluate the model's performance using model fit indices, information criteria, and reliability metrics.

Maintained by W. Jake Thompson. Last updated 2 days ago.

bayesian cdm cmdstanr cognitive-diagnosis cognitive-diagnostic-models dcm diagnostic-classification-models psychometrics rstan stan cpp

10 stars 6.81 score 31 scripts

helske

bssm:Bayesian Inference of Non-Linear and Non-Gaussian State Space Models

Efficient methods for Bayesian inference of state space models via Markov chain Monte Carlo (MCMC) based on parallel importance sampling type weighted estimators (Vihola, Helske, and Franks, 2020, <doi:10.1111/sjos.12492>), particle MCMC, and its delayed acceptance version. Gaussian, Poisson, binomial, negative binomial, and Gamma observation densities and basic stochastic volatility models with linear-Gaussian state dynamics, as well as general non-linear Gaussian models and discretised diffusion models are supported. See Helske and Vihola (2021, <doi:10.32614/RJ-2021-103>) for details.

Maintained by Jouni Helske. Last updated 7 months ago.

bayesian-inference cpp markov-chain-monte-carlo particle-filter state-space time-series openblas cpp openmp

42 stars 6.43 score 11 scripts

yoshidk6

rstanemax:Emax Model Analysis with 'Stan'

Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.

Maintained by Kenta Yoshida. Last updated 1 months ago.

cpp

5 stars 6.34 score 21 scripts 1 dependents

genentech

BayesERtools:Bayesian Exposure-Response Analysis Tools

Suite of tools that facilitate exposure-response analysis using Bayesian methods. The package provides a streamlined workflow for fitting types of models that are commonly used in exposure-response analysis - linear and Emax for continuous endpoints, logistic linear and logistic Emax for binary endpoints, as well as performing simulation and visualization. Learn more about the workflow at <https://genentech.github.io/BayesERbook/>.

Maintained by Kenta Yoshida. Last updated 1 months ago.

2 stars 4.78 score 20 scripts

weberse2

OncoBayes2:Bayesian Logistic Regression for Oncology Dose-Escalation Trials

Bayesian logistic regression model with optional EXchangeability-NonEXchangeability parameter modelling for flexible borrowing from historical or concurrent data-sources. The safety model can guide dose-escalation decisions for adaptive oncology Phase I dose-escalation trials which involve an arbitrary number of drugs. Please refer to Neuenschwander et al. (2008) <doi:10.1002/sim.3230> and Neuenschwander et al. (2016) <doi:10.1080/19466315.2016.1174149> for details on the methodology.

Maintained by Sebastian Weber. Last updated 13 days ago.

cpp

2.78 score 15 scripts