Package: multigroup.vaccine 0.1.1

Damon Toth

multigroup.vaccine: Analyze Outbreak Models of Multi-Group Populations with Vaccination

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>.

Authors:Damon Toth [aut, cre, cph], Jake Wagoner [aut], Willy Ray [aut], George Vega Yon [ctb], Centers for Disease Control and Prevention's Center for Forecasting and Outbreak Analytics [fnd]

multigroup.vaccine_0.1.1.tar.gz
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multigroup.vaccine_0.1.1.tgz(r-4.6-x86_64)multigroup.vaccine_0.1.1.tgz(r-4.6-arm64)multigroup.vaccine_0.1.1.tgz(r-4.5-x86_64)multigroup.vaccine_0.1.1.tgz(r-4.5-arm64)
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multigroup.vaccine_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
multigroup.vaccine/json (API)

# Install 'multigroup.vaccine' in R:
install.packages('multigroup.vaccine', repos = c('https://epiforesite.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/epiforesite/multigroup-vaccine/issues

Pkgdown/docs site:https://epiforesite.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

6.86 score 2 stars 19 scripts 136 downloads 1 mentions 20 exports 57 dependencies

Last updated from:5c75b45c9f. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK174
linux-devel-x86_64OK165
source / vignettesOK202
linux-release-arm64OK185
linux-release-x86_64OK163
macos-release-arm64OK103
macos-release-x86_64OK186
macos-oldrel-arm64OK82
macos-oldrel-x86_64OK267
windows-develOK155
windows-releaseOK165
windows-oldrelOK140
wasm-releaseOK121

Exports:aggregateByAgeGroupscontactMatrixAgeSchoolcontactMatrixPolymodcontactMatrixPropPreffinalsizegetCensusDatagetCensusDataPathgetCityDatagetFinalSizeAnalyticgetFinalSizeDistgetFinalSizeDistEscapegetFinalSizeODEgetSizeAtTimegetStateFIPSlistCountiesodeSIRrun_my_appsimodeSIRtransmissionRatesvaxrepnum

Dependencies:askpassbackportsbase64encbslibcachemcheckmateclicommonmarkcountrycodecpp11curldata.tabledeSolvedigestfastmapfontawesomefsgenericsgluehtmltoolshttpuvhttrjquerylibjsonlitelaterlifecyclelubridatemagrittrmemoisemimeoaiopensslotelpillarpkgconfigplyrpromisespurrrR6rappdirsRcpprlangsassshinysocialmixrsourcetoolsstringistringrsystibbletimechangeutf8vctrswithrwpp2017xml2xtable

Using Census Data Functions
Introduction | Step 1: Getting State FIPS Codes | Step 2: Listing Counties | Step 3: Retrieving Population Data | Step 4: Visualizing Age Distribution | Step 5: Comparing Multiple Counties | Step 6: Using City-Level Data (getCityData) | Example 1: Default 5-year Age Groups | Example 2: Custom Age Groups for School-Based Analysis | Visualizing the Comparison | Summary
Rendered fromcensus_functions_demo.Rmdusingknitr::rmarkdown

Last update: 2026-02-06
Started: 2026-01-14

Measles Age-Structured Model
Rendered frommeasles_agemodel.Rmdusingknitr::rmarkdown

Last update: 2026-02-02
Started: 2025-07-07

Getting Started Example
Rendered fromrun_model_on_command_line.Rmdusingknitr::rmarkdown

Last update: 2026-01-29
Started: 2025-03-04

Contact Matrix Examples
Rendered fromcontact_matrix_examples.Rmdusingknitr::rmarkdown

Last update: 2026-01-28
Started: 2025-11-20

Readme and manuals

Help Manual

Help pageTopics
Aggregate population counts into age groupsaggregateByAgeGroups
Calculate a contact matrix for age groups and schoolscontactMatrixAgeSchool
Calculate a contact matrix for age groups based on Polymod contact survey datacontactMatrixPolymod
Calculate group contact matrix with proportional mixing and preferential mixing within groupcontactMatrixPropPref
Calculate final outbreak size or distribution of a multigroup transmission model for a given basic reproduction number, contact/transmission assumptions, and initial conditionsfinalsize
Get Census Population Data by Age and CountygetCensusData
Get path to example census data filegetCensusDataPath
Get City Population Data by AgegetCityData
Calculate final size of outbreak: the total number of infections in each group, by solving the analytic final size equationgetFinalSizeAnalytic
Estimate the distribution of final outbreak sizes by group using stochastic simulations of multi-group modelgetFinalSizeDist
Estimate the distribution of final outbreak sizes by group using a hybrid model: stochastic simulations for smaller-sized outbreaks and deterministic ordinary differential equation model for "escaped" outbreaksgetFinalSizeDistEscape
Calculate outbreak final size, the total number of infections in each group, by numerically solving the multi-group ordinary differential equationgetFinalSizeODE
Calculate outbreak size at a given timegetSizeAtTime
Get state FIPS code by state namegetStateFIPS
List available counties for a statelistCounties
Ordinary differential equation function for multi-group susceptible-infectious-removed (SIR) model used as "func" argument passed to the ode() function from deSolve packageodeSIR
Runs the shiny apprun_my_app
Calculate time trajectory of solution to a Susceptible-Infectious-Removed (SIR) system by numerically solving the multi-group ordinary differential equationssimodeSIR
Calculate transmission rate matrix for multi-group model with specified R0transmissionRates
Calculate reproduction number for a multigroup model with a given state of vaccination and immunityvaxrepnum