HHBayes

0.1.1

Bayesian Household Transmission Modeling with 'Stan'

0packages depend

1.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Ke LiFirst published 2026-04-101 releasesCRAN page ↗GitHub ↗

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).

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("HHBayes", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("keli5734/HHBayes")

Development version from keli5734/HHBayes. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-hhbayes

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-HHBayes

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-HHBayes

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 8.3 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-04-11
2 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,979 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

1.7K

CRAN downloads in the past year

Rank #7,127 · ~5/day · ~141/mo

Releases R versions

Daily download trend is not available in this view yet.

42330 days

1.5K90 days

1.7K1 year

Compare downloads with other packages →

Also on104 r2u12 autocran

Repository

GitHub ↗ keli5734/hhbayes

6Stars

1Forks

0Open issues

0Open PRs

0Releases

70Commits

1Contributors

70 commits · Last activity 2026-04-27 · 0% stars, 30d

Stars over time

2026-03-31 · 32026-07-07 · 6

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/keli5734/hhbayes on 2026-07-19.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4.0

Imports (11)

methodsRcpp rstan rstantools (>= 2.4.0)dplyr ggplot2 tidyr ggpubr scales deSolve rlang

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.18.0)

Suggests (4)

knitr rmarkdown RcppParallel cowplot

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 2,787 (40%)C 2,546 (36%)Rd 802 (11%)Vignettes 784 (11%)C++ 57 (1%)

Code characteristics

Cyclomatic complexity: 3.5 median / 85 max
System requirements: 1 external

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

29 12 exported

Complexity

11.2 avg / 85 max

Call network

29 nodes / 15 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)

Maintainer (1)

Ke Li

Author, Maintainer

Authors (2)

Ke Li

Author, Maintainer

Yiren Hou

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.1Latest
2026-04-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-10
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.4.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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