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:
Downloads:
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