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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 (may not be active yet) |
| 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:
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=HHBayes
to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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