measr
measr: Bayesian psychometric measurement using Stan - Published in JOSS (2023)
geostan
geostan: An R package for Bayesian spatial analysis - Published in JOSS (2022)
The stantargets R package
The stantargets R package: a workflow framework for efficient reproducible Stan-powered Bayesian data analysis pipelines - Published in JOSS (2021)
epinow2
Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
epinowcast
Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes.
brms
brms R package for Bayesian generalized multivariate non-linear multilevel models using Stan
DiffEqBayes
Extension functionality which uses Stan.jl, DynamicHMC.jl, and Turing.jl to estimate the parameters to differential equations and perform Bayesian probabilistic scientific machine learning
mvgam
{mvgam} R 📦 to fit Dynamic Bayesian Generalized Additive Models for multivariate modeling and forecasting
https://github.com/biocore/birdman
Bayesian Inferential Regression for Differential Microbiome Analysis
LMMELSM
R Package for fitting latent multivariate mixed effects location scale models.
MIRES
R package for Bayesian measurement invariance assessment using mixed effects and shrinkage.
https://github.com/cdcgov/ww-inference-model
An in-development R package and a Bayesian hierarchical model jointly fitting multiple "local" wastewater data streams and "global" case count data to produce nowcasts and forecasts of both observations
physalia-forecasting-course
Ecological forecasting using Dynamic Generalized Additive Models with R 📦's {mvgam} and {brms}
lgpr
R-package for interpretable nonparametric modeling of longitudinal data using additive Gaussian processes. Contains functionality for inferring covariate effects and assessing covariate relevances. Various models can be specified using a convenient formula syntax.
https://github.com/4ment/gradient-benchmark
automatic/analytical differentiation benchmark
deb_individualvariability-palmer-et-al.2024
DEB_IndividualVariability Palmer et al. 2024
r-pipeline-development-workshop
Workshop on pipeline development and model deployment onto Kubernetes via Docker using R.
hmde
Implementation of hierarchical Bayesian longitudinal models to estimate differential equation parameters.
hookworm_anaemia_statistical_model
Statistical model to simulate individual haemoglobin concentrations in human hosts as a function of observed egg counts quantifying hookworm infection. The model employs latent variables to reproduce an underlying worm burdens distribution in the population. The model after calibration is used to predict the prevalence of anaemia that can be attributed to hookworm infection.
coevolve
coevolve R package for Bayesian generalized dynamic phylogenetic models using Stan
ubms
Fit models to data from unmarked animals using Stan. Uses a similar interface to the R package 'unmarked', while providing the advantages of Bayesian inference and allowing estimation of random effects.
https://github.com/bonstats/undecided-voters-us-pres-elections
Data and code for "Polling bias and undecided voter allocations: US Presidential elections, 2004 - 2016"
