HHBayes: Bayesian Household Transmission Modeling with 'Stan'

Provides a streamlined pipeline to simulate household infection dynamics, estimate transmission parameters, and visualize epidemic timelines. Uses a Bayesian approach with 'Stan' that models transmission probability as a function of viral load, seasonality and infectivity, multiple infection episodes (reinfections), and waning immunity modeling. Li et al. (2026) <doi:10.64898/2026.04.01.26349903>).

Version:	0.1.1
Depends:	R (≥ 3.4.0)
Imports:	methods, Rcpp (≥ 0.12.0), rstan (≥ 2.18.1), rstantools (≥ 2.4.0), dplyr, ggplot2, tidyr, ggpubr, scales, deSolve, rlang
LinkingTo:	BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), StanHeaders (≥ 2.18.0)
Suggests:	knitr, rmarkdown, RcppParallel (≥ 5.0.1), cowplot
Published:	2026-04-10
DOI:	10.32614/CRAN.package.HHBayes
Author:	Ke Li [aut, cre], Yiren Hou [aut]
Maintainer:	Ke Li <ke.li.kl662 at yale.edu>
BugReports:	https://github.com/keli5734/HHBayes/issues
License:	MIT + file LICENSE
URL:	https://github.com/keli5734/HHBayes
NeedsCompilation:	yes
SystemRequirements:	GNU make
Materials:	README, NEWS
CRAN checks:	HHBayes results

Documentation:

Reference manual:	HHBayes.html , HHBayes.pdf
Vignettes:	Getting Started with HHBayes (source, R code)

Downloads:

Package source:	HHBayes_0.1.1.tar.gz
Windows binaries:	r-devel: HHBayes_0.1.1.zip, r-release: HHBayes_0.1.1.zip, r-oldrel: HHBayes_0.1.1.zip
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): HHBayes_0.1.1.tgz, r-oldrel (x86_64): HHBayes_0.1.1.tgz

Linking:

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