{ "_id": "6a1f29afb401979e7342416a", "Package": "multigroup.vaccine", "Type": "Package", "Title": "Analyze Outbreak Models of Multi-Group Populations with\nVaccination", "Version": "0.2.0", "Authors@R": "c(person(\"Damon\", \"Toth\", , \"damon.toth@hsc.utah.edu\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-7393-4814\")),\nperson(\"Jake\", \"Wagoner\", , \"jakew@sci.utah.edu\", role = c(\"aut\"),\ncomment = c(ORCID = \"0009-0000-5053-2281\")),\nperson(\"Willy\", \"Ray\", , \"william.ray@hsc.utah.edu\", role = c(\"aut\")),\nperson(\"George\", \"Vega Yon\", , \"g.vegayon@gmail.com\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-3171-0844\")),\nperson(\"Centers for Disease Control and Prevention's Center for Forecasting and Outbreak Analytics\",\nrole=\"fnd\", comment = \"Cooperative agreement CDC-RFA-FT-23-0069\"))", "Description": "Model infectious disease dynamics in populations with\nmultiple subgroups having different vaccination rates,\ntransmission characteristics, and contact patterns. Calculate\nfinal and intermediate outbreak sizes, form age-structured\ncontact models with automatic fetching of U.S. census data, and\nexplore vaccination scenarios with an interactive 'shiny'\ndashboard for a model with two subgroups, as described in\nNguyen et al. (2024) and Duong\net al. (2026) .", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE)", "URL": "https://epiforesite.github.io/multigroup-vaccine/", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libxml2-dev\nlibssl-dev zlib1g-dev", "Repository": "https://epiforesite.r-universe.dev", "Date/Publication": "2026-05-15 21:48:19 UTC", "RemoteUrl": "https://github.com/EpiForeSITE/multigroup-vaccine", "RemoteRef": "HEAD", "RemoteSha": "f2d81b13bd9e51088962498528ab981916522e6c", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-15 22:07:48 UTC", "User": "root" }, "Author": "Damon Toth [aut, cre, cph] (ORCID:\n),\nJake Wagoner [aut] (ORCID: ),\nWilly Ray [aut],\nGeorge Vega Yon [ctb] (ORCID: ),\nCenters for Disease Control and Prevention's Center for Forecasting and\nOutbreak Analytics [fnd] (Cooperative agreement CDC-RFA-FT-23-0069)", "Maintainer": "Damon Toth ", "MD5sum": "ba56eaa7e3dd89e30678fa2561ac8385", "_user": "epiforesite", "_type": "src", "_file": "multigroup.vaccine_0.2.0.tar.gz", "_fileid": "ce5626eec35f8a47b036306269ea364763df054cde161c2b30188dcff0fbf671", "_filesize": 798751, "_sha256": "ce5626eec35f8a47b036306269ea364763df054cde161c2b30188dcff0fbf671", "_created": "2026-05-15T22:07:48.000Z", "_published": "2026-06-02T19:06:23.711Z", "_distro": "noble", "_jobs": [ { "job": 79150444958, "time": 158, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7027434771" }, { "job": 79150444343, "time": 169, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7027437405" }, { "job": 79150445070, "time": 165, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7027436357" }, { "job": 79150445322, "time": 160, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7027435100" }, { "job": 79150445361, "time": 113, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7027425424" }, { "job": 79150444957, "time": 179, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7027439449" }, { "job": 79150445248, "time": 132, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7027429342" }, { "job": 79150444963, "time": 222, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7027449064" }, { "job": 79150443783, "time": 199, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7027400670" }, { "job": 79150443996, "time": 124, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7367282254" }, { "job": 79150445149, "time": 174, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7027438379" }, { "job": 79150444909, "time": 125, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7027427925" }, { "job": 79150445106, "time": 120, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7027426700" } ], "_buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/EpiForeSITE/multigroup-vaccine", "_commit": { "id": "f2d81b13bd9e51088962498528ab981916522e6c", "author": "damontoth ", "committer": "GitHub ", "message": "Update to replace deprecated socialmixr elements; resolves #77 (#80)\n\n* Replace defunct argument names to socialmixr::contact_matrix()\n\n* add updated Polymod country population data and edit contactMatrixPolymod() to use it", "time": 1778881699 }, "_maintainer": { "name": "Damon Toth", "email": "damon.toth@hsc.utah.edu", "login": "damontoth", "uuid": 16004052, "orcid": "0000-0001-7393-4814" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "deSolve", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "bslib", "version": ">= 0.9.0", "role": "Imports" }, { "package": "htmltools", "role": "Imports" }, { "package": "socialmixr", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "epiforesite", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-20", "n": 16 }, { "week": "2025-21", "n": 2 }, { "week": "2025-22", "n": 11 }, { "week": "2025-24", "n": 2 }, { "week": "2025-25", "n": 5 }, { "week": "2025-28", "n": 7 }, { "week": "2025-35", "n": 1 }, { "week": "2025-45", "n": 2 }, { "week": "2025-46", "n": 3 }, { "week": "2025-47", "n": 3 }, { "week": "2025-48", "n": 4 }, { "week": "2025-50", "n": 3 }, { "week": "2025-51", "n": 2 }, { "week": "2026-03", "n": 3 }, { "week": "2026-04", "n": 2 }, { "week": "2026-05", "n": 13 }, { "week": "2026-06", "n": 6 }, { "week": "2026-10", "n": 2 }, { "week": "2026-18", "n": 1 }, { "week": "2026-19", "n": 1 }, { "week": "2026-20", "n": 1 } ], "_tags": [ { "name": "v0.1.1", "date": "2026-02-06" } ], "_stars": 2, "_contributors": [ { "user": "damontoth", "count": 85, "uuid": 16004052 }, { "user": "willyray", "count": 71, "uuid": 11864373 }, { "user": "jakewags", "count": 18, "uuid": 35744963 }, { "user": "gvegayon", "count": 5, "uuid": 893619 }, { "user": "copilot", "count": 2, "uuid": 198982749 }, { "user": "apulsipher", "count": 1, "uuid": 45372570 } ], "_userbio": { "uuid": 158560900, "type": "organization", "name": "ForeSITE", "description": "A collection of epidemic modeling and forecasting tools for ForeSITE, part of the CDC-funded InsightNet" }, "_downloads": { "count": 224, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/multigroup.vaccine" }, "_mentions": 1, "_devurl": "https://github.com/epiforesite/multigroup-vaccine", "_pkgdown": "https://epiforesite.github.io/multigroup-vaccine/", "_searchresults": 20, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/multigroup.vaccine.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/epiforesite/multigroup-vaccine", "_realowner": "epiforesite", "_cranurl": true, "_releases": [ { "version": "0.1.1", "date": "2026-02-16" } ], "_exports": [ "aggregateByAgeGroups", "contactMatrixAgeSchool", "contactMatrixPolymod", "contactMatrixPropPref", "finalsize", "getCensusData", "getCensusDataPath", "getCityData", "getFinalSizeAnalytic", "getFinalSizeDist", "getFinalSizeDistEscape", "getFinalSizeODE", "getSizeAtTime", "getStateFIPS", "listCounties", "odeSIR", "run_my_app", "simodeSIR", "transmissionRates", "vaxrepnum" ], "_help": [ { "page": "aggregateByAgeGroups", "title": "Aggregate population counts into age groups", "topics": [ "aggregateByAgeGroups" ] }, { "page": "contactMatrixAgeSchool", "title": "Calculate a contact matrix for age groups and schools", "topics": [ "contactMatrixAgeSchool" ] }, { "page": "contactMatrixPolymod", "title": "Calculate a contact matrix for age groups based on Polymod contact survey data", "topics": [ "contactMatrixPolymod" ] }, { "page": "contactMatrixPropPref", "title": "Calculate group contact matrix with proportional mixing and preferential mixing within group", "topics": [ "contactMatrixPropPref" ] }, { "page": "finalsize", "title": "Calculate final outbreak size or distribution of a multigroup transmission model for a given basic reproduction number, contact/transmission assumptions, and initial conditions", "topics": [ "finalsize" ] }, { "page": "getCensusData", "title": "Get Census Population Data by Age and County", "topics": [ "getCensusData" ] }, { "page": "getCensusDataPath", "title": "Get path to example census data file", "topics": [ "getCensusDataPath" ] }, { "page": "getCityData", "title": "Get City Population Data by Age", "topics": [ "getCityData" ] }, { "page": "getFinalSizeAnalytic", "title": "Calculate final size of outbreak: the total number of infections in each group, by solving the analytic final size equation", "topics": [ "getFinalSizeAnalytic" ] }, { "page": "getFinalSizeDist", "title": "Estimate the distribution of final outbreak sizes by group using stochastic simulations of multi-group model", "topics": [ "getFinalSizeDist" ] }, { "page": "getFinalSizeDistEscape", "title": "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\" outbreaks", "topics": [ "getFinalSizeDistEscape" ] }, { "page": "getFinalSizeODE", "title": "Calculate outbreak final size, the total number of infections in each group, by numerically solving the multi-group ordinary differential equation", "topics": [ "getFinalSizeODE" ] }, { "page": "getSizeAtTime", "title": "Calculate outbreak size at a given time", "topics": [ "getSizeAtTime" ] }, { "page": "getStateFIPS", "title": "Get state FIPS code by state name", "topics": [ "getStateFIPS" ] }, { "page": "listCounties", "title": "List available counties for a state", "topics": [ "listCounties" ] }, { "page": "odeSIR", "title": "Ordinary differential equation function for multi-group susceptible-infectious-removed (SIR) model used as \"func\" argument passed to the ode() function from deSolve package", "topics": [ "odeSIR" ] }, { "page": "run_my_app", "title": "Runs the shiny app", "topics": [ "run_my_app" ] }, { "page": "simodeSIR", "title": "Calculate time trajectory of solution to a Susceptible-Infectious-Removed (SIR) system by numerically solving the multi-group ordinary differential equations", "topics": [ "simodeSIR" ] }, { "page": "transmissionRates", "title": "Calculate transmission rate matrix for multi-group model with specified R0", "topics": [ "transmissionRates" ] }, { "page": "vaxrepnum", "title": "Calculate reproduction number for a multigroup model with a given state of vaccination and immunity", "topics": [ "vaxrepnum" ] } ], "_readme": "https://github.com/EpiForeSITE/multigroup-vaccine/raw/HEAD/README.md", "_rundeps": [ "askpass", "backports", "base64enc", "bslib", "cachem", "checkmate", "cli", "commonmark", "countrycode", "cpp11", "curl", "data.table", "deSolve", "digest", "fastmap", "fontawesome", "fs", "generics", "glue", "htmltools", "httpuv", "httr", "jquerylib", "jsonlite", "later", "lifecycle", "lubridate", "magrittr", "memoise", "mime", "oai", "openssl", "otel", "pillar", "pkgconfig", "plyr", "promises", "purrr", "R6", "rappdirs", "Rcpp", "rlang", "sass", "shiny", "socialmixr", "sourcetools", "stringi", "stringr", "sys", "tibble", "timechange", "utf8", "vctrs", "withr", "wpp2017", "xml2", "xtable" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "contact_matrix_examples.Rmd", "filename": "contact_matrix_examples.html", "title": "Contact Matrix Examples", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-11-20 21:02:34", "modified": "2026-01-28 19:20:45", "commits": 4 }, { "source": "run_model_on_command_line.Rmd", "filename": "run_model_on_command_line.html", "title": "Getting Started Example", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-03-04 20:51:39", "modified": "2026-01-29 19:12:56", "commits": 12 }, { "source": "measles_agemodel.Rmd", "filename": "measles_agemodel.html", "title": "Measles Age-Structured Model", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-07-07 20:33:57", "modified": "2026-02-02 23:10:50", "commits": 6 }, { "source": "census_functions_demo.Rmd", "filename": "census_functions_demo.html", "title": "Using Census Data Functions", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2026-01-14 23:08:40", "modified": "2026-02-06 19:36:59", "commits": 2 } ], "_score": 6.924279286061882, "_indexed": true, "_nocasepkg": "multigroup.vaccine", "_universes": [ "epiforesite", "damontoth" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-05-15T22:10:15.000Z", "distro": "noble", "arch": "aarch64", "commit": "f2d81b13bd9e51088962498528ab981916522e6c", "fileid": "154f1abfad7353bb49f8b5253beb77e05d46e2b5e4feac5fc72bf7d2f9c341a4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929" }, { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-05-15T22:10:06.000Z", "distro": "noble", "arch": "x86_64", "commit": "f2d81b13bd9e51088962498528ab981916522e6c", "fileid": "e1ca6582a7fa7cdb9db92779a6395d0f3e384cdba5b076c25030f05960391412", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929" }, { "r": "4.6.0", "os": "linux", "version": "0.2.0", "date": "2026-05-15T22:10:21.000Z", "distro": "noble", "arch": "aarch64", "commit": "f2d81b13bd9e51088962498528ab981916522e6c", "fileid": "17f0b65081a872efa0552b1cb230f1b91c8b33c53e1580d19e4f89e4e7ee4d18", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929" }, { "r": "4.6.0", "os": "linux", "version": "0.2.0", "date": "2026-05-15T22:10:11.000Z", "distro": "noble", "arch": "x86_64", "commit": "f2d81b13bd9e51088962498528ab981916522e6c", "fileid": "886f332beed28f285851795bddc940ca7e1d488ebf79f4206c2152aeda8ff8cb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929" }, { "r": "4.5.3", "os": "mac", "version": "0.2.0", "date": "2026-05-15T22:09:33.000Z", "arch": "aarch64", "commit": "f2d81b13bd9e51088962498528ab981916522e6c", "fileid": "168c1c4e460031aea42231a51fefa4784ae35d00186b4b66ac1987827fc42904", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929" }, { "r": "4.5.3", "os": "mac", "version": "0.2.0", "date": "2026-05-15T22:10:12.000Z", "arch": "x86_64", "commit": "f2d81b13bd9e51088962498528ab981916522e6c", "fileid": "157e707ef007012eb3171b8b40ce68a99aea0a1f1834d3cac04557d5411012dd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929" }, { "r": "4.6.0", "os": "mac", "version": "0.2.0", "date": "2026-05-15T22:09:43.000Z", "arch": "aarch64", "commit": "f2d81b13bd9e51088962498528ab981916522e6c", "fileid": "aed16f1002e09e04ac516046c490374c55b6dbf67aeeccaece9c78484526bb58", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929" }, { "r": "4.6.0", "os": "mac", "version": "0.2.0", "date": "2026-05-15T22:10:56.000Z", "arch": "x86_64", "commit": "f2d81b13bd9e51088962498528ab981916522e6c", "fileid": "46adec3dbb01d2e951cfa157c1f87dcdc72b2c99bc3ca36e5a6feba6736e240e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929" }, { "r": "4.7.0", "os": "win", "version": "0.2.0", "date": "2026-05-15T22:09:33.000Z", "arch": "x86_64", "commit": "f2d81b13bd9e51088962498528ab981916522e6c", "fileid": "8ba4091a440a04ee9b18d2856b31f38074031d5767d57834c53564de4212ee3d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929" }, { "r": "4.5.3", "os": "win", "version": "0.2.0", "date": "2026-05-15T22:09:09.000Z", "arch": "x86_64", "commit": "f2d81b13bd9e51088962498528ab981916522e6c", "fileid": "ae258715771f26231e307bc8e2c275c67e68f13f609dd7aa2ce90b932ec0968d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929" }, { "r": "4.6.0", "os": "win", "version": "0.2.0", "date": "2026-05-15T22:09:04.000Z", "arch": "x86_64", "commit": "f2d81b13bd9e51088962498528ab981916522e6c", "fileid": "60b9e0c19bd5e2244cce565f59c33968c9397754e02221a0ab895f2cc6be6f99", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.0", "date": "2026-06-02T19:06:01.000Z", "arch": "emscripten", "commit": "f2d81b13bd9e51088962498528ab981916522e6c", "fileid": "185a8de5e8e0debe9bc6891db902b1428beef62e3cdad76bcf57736d25a935aa", "status": "success", "buildurl": "https://github.com/r-universe/epiforesite/actions/runs/25943616929" } ] }