Package: HHBayes
Title: Bayesian Household Transmission Modeling with 'Stan'
Version: 0.1.1
Authors@R: c(
  person(given = "Ke", family = "Li",
         email = "ke.li.kl662@yale.edu",
         role = c("aut","cre"),
         comment = c(ORCID = "0000-0002-1252-670X")),
  person(given = "Yiren", family = "Hou",
         email = "yiren.hou@yale.edu",
         role = "aut",
         comment = c(ORCID = "0009-0005-0422-4268"))
	)
Description: 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>).
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.3
Biarch: true
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)
SystemRequirements: GNU make
Suggests: knitr, rmarkdown, RcppParallel (>= 5.0.1), cowplot
VignetteBuilder: knitr
URL: https://github.com/keli5734/HHBayes
BugReports: https://github.com/keli5734/HHBayes/issues
NeedsCompilation: yes
Packaged: 2026-04-06 13:53:57 UTC; yh785
Author: Ke Li [aut, cre] (ORCID: <https://orcid.org/0000-0002-1252-670X>),
  Yiren Hou [aut] (ORCID: <https://orcid.org/0009-0005-0422-4268>)
Maintainer: Ke Li <ke.li.kl662@yale.edu>
Repository: CRAN
Date/Publication: 2026-04-10 14:00:07 UTC
Built: R 4.5.3; x86_64-w64-mingw32; 2026-06-08 05:33:11 UTC; windows
Archs: x64
