multigroup.vaccine

0.1.1

Analyze Outbreak Models of Multi-Group Populations with Vaccination

0packages depend

1.2Kdownloads / year

80.9%test coverage

13/13checks pass

Overview

About

Maintained by Damon TothFirst published 2026-02-091 releasesCRAN page ↗

Model infectious disease dynamics in populations with multiple subgroups having different vaccination rates, transmission characteristics, and contact patterns. Calculate final and intermediate outbreak sizes, form age-structured contact models with automatic fetching of U.S. census data, and explore vaccination scenarios with an interactive 'shiny' dashboard for a model with two subgroups, as described in Nguyen et al. (2024) doi:10.1016/j.jval.2024.03.039 and Duong et al. (2026) doi:10.1093/ofid/ofaf695.217.

Install

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

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

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

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-multigroup.vaccine

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-multigroup.vaccine

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-multigroup.vaccine

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

Health

CRAN checks

13OK

Slowest check: 17.7 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 2.53

80.9%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 422 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 89%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

1.2K

CRAN downloads in the past year

Rank #21,274 · ~3/day · ~101/mo

Releases R versions

Daily download trend is not available in this view yet.

22730 days

53890 days

1.2K1 year

Compare downloads with other packages →

Also on30 r2u33 autocran

Repository

GitHub ↗ epiforesite/multigroup-vaccine

2Stars

0Forks

6Open issues

2Open PRs

1Releases

185Commits

6Contributors

185 commits · Last activity 2026-07-14 · 0% stars, 30d

Stars over time

2025-02-25 · 12026-07-07 · 2

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/epiforesite/multigroup-vaccine on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Automation and maintenance (1)

pre-commit

Lint, format, editor (1)

lintr

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (7)

deSolvegraphicsshinystatsbslib htmltools socialmixr

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Damon Toth

Author, Maintainer, Copyright holder

Authors (3)

Damon Toth

Author, Maintainer, Copyright holder

Willy Ray

Author

Jake Wagoner

Author

Contributors (1)

George Vega Yon

Contributor

Damon Toth

Author, Maintainer, Copyright holder

Funders (1)

Centers for Disease Control and Prevention's Center for Forecasting and Outbreak Analytics

Funder

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-09
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Download size: 451 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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