nimble
A system for writing hierarchical statistical models largely compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do basic R-style math, and compiling both models and nimbleFunctions via custom-generated C++. 'NIMBLE' includes default methods for MCMC, Laplace Approximation, Monte Carlo Expectation Maximization, and some other tools. The nimbleFunction system makes it easy to do things like implement new MCMC samplers from R, customize the assignment of samplers to different parts of a model from R, and compile the new samplers automatically via C++ alongside the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New distributions and functions can be added, including as calls to external compiled code. Although most people think of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at <https://r-nimble.org>.
- nimbleCarbon
- saeHB
- nimbleAPT
- nimbleEcology
- tidycensus
- NumPyro
- nmaplateplot
- stableGR
- bcgam
- CODA
- dlm
- Automated parameter blocking for efficient Markov chain Monte Carlo sampling
- INLA
- BUGS
- Spatio-temporal change of support modeling with \texttt{R}
- R-INLA
- rjags
- JAGS
- mcmcse
- OpenBUGS
- AD Model Builder
- Nested adaptation of MCMC algorithms
- mvabund
- Bridging randomized controlled trials and single-arm trials using commensurate priors in arm-based network meta-analysis
- Continuous-time discrete-state modeling for deep whale dives
- MSPOCK: alleviating spatial confounding in multivariate disease mapping models
- Bayesian model assessment for jointly modeling multidimensional response data with application to computerized testing
- Rank-normalization, folding, and localization: an improved \(\widehat{R}\) for assessing convergence of MCMC (with Discussion)
- Bayesian adjustment for preferential testing in estimating infection fatality rates, as motivated by the COVID-19 pandemic
- Greater than the sum of its parts: computationally flexible Bayesian hierarchical modeling
- spBayes
- Stan
- Copula particle filters
- A multivariate spatiotemporal change-point model of opioid overdose deaths in Ohio
- pomp
- A flexible class of parametric distributions for Bayesian linear mixed models
- covreg
- Mixtures of multivariate restricted skew-normal factor analyzer models in a Bayesian framework
- LaplacesDemon
- Efficient sequential Monte Carlo algorithms for integrated population models
- RStan
- Program MARK
- RMark
- marked
- unmarked
- PRESENCE
- KFAS
- SimInf
- CARBayes
- convoSPAT
- RSpectra
- mvQuad
- rstan
- TeachingDemos
- TMB
- mra
- versions
- shinystan
- ngspatial
- secr
- BayesianTools
- LibBi
- Biips
- vSMC
- AHMbook
- scoringRules
- bridgesampling
- Bayesian semiparametric latent variable model with DP prior for joint analysis: Implementation with nimble
- mcmcplots
- CitNetExplorer
- arm
- MARK
- Gibbsit
- dobson
- t.f
- overlapping
- BayesNSGP
- factorstochvol
- tidybayes
- epimdr
- MultiBUGS
- meanShiftR
- bayest
- ADVI
- Computational Bayesian statistics. An introduction
- Bayesian joint analysis using a semiparametric latent variable model with non-ignorable missing covariates for CHNS data
- Bayesian inference for high-dimensional nonstationary Gaussian processes
- Bayesian Estimation for Bivariate Gamma Processes with Copula
- Bayesian analyses of an exponential-Poisson and related zero augmented type models
- Using R for Bayesian spatial and spatio-temporal health modeling
- A hierarchical framework for correcting under-reporting in count data
- Spatially dependent multiple testing under model misspecification, with application to detection of anthropogenic influence on extreme climate events
- glmm
- pycno
- areal
- CAM3
- spOccupancy
- ubms
- Stochastic gradient Markov chain Monte Carlo
- Time series analysis for the state-space model with R/Stan
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