{ "_id": "6ac95a1ade46216d5edda6d0", "Package": "measles", "Type": "Package", "Title": "Measles Epidemiological Models", "Version": "0.4.1-0", "Authors@R": "c(\nperson(given=\"George\", family=\"Vega Yon\", role=c(\"aut\", \"cre\"),\nemail=\"g.vegayon@gmail.com\", comment = c(ORCID = \"0000-0002-3171-0844\")),\nperson(\n\"Damon\", \"Toth\", email = \"damon.toth@hsc.utah.edu\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0001-7393-4814\")\n),\nperson(\n\"Jake\", \"Wagoner\", email = \"jakew@sci.utah.edu\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0009-0000-5053-2281\")\n),\nperson(\n\"Olivia\", \"Banks\", email = \"olivia.banks@utah.edu\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0009-0008-7611-6030\")\n),\nperson(\"Centers for Disease Control and Prevention\", role=\"fnd\", comment = \"Award number 1U01CK000585; 75D30121F00003\"\n))", "Description": "A specialized collection of measles epidemiological models\nbuilt on the 'epiworldR' framework. This package is a spinoff\nfrom 'epiworldR' focusing specifically on measles transmission\ndynamics. It includes models for school settings with\nquarantine and isolation policies, mixing models with\npopulation groups, and risk-based quarantine strategies. The\nmodels use Agent-Based Models (ABM) with a fast 'C++' backend\nfrom the 'epiworld' library. Ideal for studying measles\noutbreaks, vaccination strategies, and intervention policies.", "URL": "https://github.com/UofUEpiBio/measles", "BugReports": "https://github.com/UofUEpiBio/measles/issues", "License": "MIT + file LICENSE", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "SystemRequirements": "C++17", "VignetteBuilder": "quarto", "LazyData": "true", "Additional_repositories": "https://uofuepibio.r-universe.dev", "Remotes": [ "UofUEpiBio/epiworldR" ], "Repository": "https://uofuepibio.r-universe.dev", "Date/Publication": "2026-10-09 19:59:26 UTC", "RemoteUrl": "https://github.com/UofUEpiBio/measles", "RemoteRef": "HEAD", "RemoteSha": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-09 21:08:09 UTC", "User": "root" }, "Author": "George Vega Yon [aut, cre] (ORCID:\n),\nDamon Toth [ctb] (ORCID: ),\nJake Wagoner [ctb] (ORCID: ),\nOlivia Banks [ctb] (ORCID: ),\nCenters for Disease Control and Prevention [fnd] (Award number\n1U01CK000585; 75D30121F00003)", "Maintainer": "George Vega Yon ", "_user": "uofuepibio", "_type": "src", "_file": "measles_0.4.1-0.tar.gz", "_fileid": "https://r2.ropensci.org/b6dc272d1a683d23d5d41dd9c979b79e676602e1e6023fd2336fc1b13c66d5b3", "_filesize": 1828665, "_sha256": "b6dc272d1a683d23d5d41dd9c979b79e676602e1e6023fd2336fc1b13c66d5b3", "_expires": "2027-01-17T21:18:16.000Z", "_created": "2026-10-09T21:08:09.000Z", "_published": "2026-10-09T21:18:18.529Z", "_buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 114026903113, "time": 145, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11645272755" }, { "job": 114026903197, "time": 156, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11645073755" }, { "job": 114026903062, "time": 149, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11644804142" }, { "job": 114026903165, "time": 151, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11645412480" }, { "job": 114026903193, "time": 199, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11645402745" }, { "job": 114026903066, "time": 249, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11645357968" }, { "job": 114026903129, "time": 182, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11645935181" }, { "job": 114026903055, "time": 355, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11645512737" }, { "job": 114025361059, "time": 253, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11645651509" }, { "job": 114026902948, "time": 108, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11645217851" }, { "job": 114026903206, "time": 483, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11645413266" }, { "job": 114026903252, "time": 230, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11645452624" }, { "job": 114026903294, "time": 178, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11645432393" }, { "job": 114026903213, "time": 556, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11645538228" }, { "job": 114026903285, "time": 243, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11644699937" } ], "_upstream": "https://github.com/UofUEpiBio/measles", "_commit": { "id": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "author": "George G. Vega Yon ", "committer": "GitHub ", "message": "Label parameters without a published source as assumptions (#64)\n\nThe hospitalization rate, the tiered quarantine lengths, and the\nwillingness and contact-tracing parameters are now attributed to\n'Assumption', without reference to decisions by partners or field\nexperience.\n\nCo-authored-by: Claude Opus 5.5 ", "time": 1791575966 }, "_maintainer": { "name": "George Vega Yon", "email": "g.vegayon@gmail.com", "login": "gvegayon", "bluesky": "@gvegayon.bsky.social", "linkedin": "in/georgevegayon", "description": "Scientist at @UofUEpiBio modeling complex systems using statistical computing. Lots of time at @CDCgov.", "uuid": 893619, "orcid": "0000-0002-3171-0844" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "epiworldR", "version": ">= 0.19.0", "role": "Depends" }, { "package": "cpp11", "role": "LinkingTo" }, { "package": "epiworldR", "version": ">= 0.19.0", "role": "LinkingTo" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tinytest", "role": "Suggests" }, { "package": "data.table", "role": "Suggests" }, { "package": "quarto", "role": "Suggests" }, { "package": "multigroup.vaccine", "role": "Suggests" } ], "_owner": "uofuepibio", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-42", "n": 3 }, { "week": "2025-43", "n": 1 }, { "week": "2025-45", "n": 4 }, { "week": "2025-46", "n": 14 }, { "week": "2025-47", "n": 4 }, { "week": "2025-49", "n": 5 }, { "week": "2025-50", "n": 4 }, { "week": "2025-51", "n": 6 }, { "week": "2026-05", "n": 1 }, { "week": "2026-07", "n": 1 }, { "week": "2026-08", "n": 1 }, { "week": "2026-09", "n": 2 }, { "week": "2026-11", "n": 1 }, { "week": "2026-13", "n": 1 }, { "week": "2026-14", "n": 1 }, { "week": "2026-15", "n": 2 }, { "week": "2026-16", "n": 2 }, { "week": "2026-17", "n": 4 }, { "week": "2026-29", "n": 1 }, { "week": "2026-31", "n": 1 }, { "week": "2026-32", "n": 1 }, { "week": "2026-33", "n": 1 }, { "week": "2026-36", "n": 1 }, { "week": "2026-37", "n": 3 }, { "week": "2026-39", "n": 2 }, { "week": "2026-41", "n": 6 } ], "_tags": [ { "name": "v0.1.0", "date": "2026-02-12" }, { "name": "v0.1.1", "date": "2026-02-18" }, { "name": "v0.2.0", "date": "2026-03-31" } ], "_topics": [ "abm", "agent-based-modeling", "epidemiology", "individual-based-modelling", "measles", "measles-mumps-rubella-vaccine", "r-programming", "simulation", "quarto", "cpp" ], "_stars": 5, "_contributors": [ { "user": "gvegayon", "count": 274, "uuid": 893619 }, { "user": "derekmeyer37", "count": 123, "uuid": 105825983 }, { "user": "apulsipher", "count": 25, "uuid": 45372570 }, { "user": "copilot", "count": 15, "uuid": 198982749 }, { "user": "abinashbunty", "count": 1, "uuid": 25522048 } ], "_userbio": { "uuid": 89941410, "type": "organization", "name": "Divisions of Epidemiology and Biostatistics at the U", "followers": 13 }, "_downloads": { "count": 348, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/measles" }, "_devurl": "https://github.com/uofuepibio/measles", "_searchresults": 14, "_quarto": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/measles.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/uofuepibio/measles", "_realowner": "uofuepibio", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2026-02-16" }, { "version": "0.1.1", "date": "2026-02-21" }, { "version": "0.2.0", "date": "2026-03-31" } ], "_exports": [ "calibrate_mixing_model", "InterventionMeaslesPEP", "make_cmat_symmetric", "measles_cpp_version", "measles_parameters", "ModelMeaslesMixing", "ModelMeaslesMixingRiskQuarantine", "ModelMeaslesQuarantine", "ModelMeaslesSchool" ], "_datasets": [ { "name": "short_creek", "title": "Short Creek Population Data by Age Group", "object": "short_creek", "class": [ "data.table", "data.frame" ], "fields": [ "age_labels", "agepops", "agelims", "vacc_rate" ], "rows": 15, "table": true, "tojson": true }, { "name": "short_creek_matrix", "title": "Short Creek Mixing Matrix", "object": "short_creek_matrix", "class": [ "matrix", "array" ], "fields": [ "under1", "1to4", "5to11s1", "5to11s2", "5to11s3", "12to13s4", "12to13s5", "12to13s6", "14to17s7", "14to17s8", "14to17s9", "18to24", "25to44", "45to69", "70+" ], "rows": 15, "table": true, "tojson": true } ], "_help": [ { "page": "calibrate_mixing_model", "title": "Calibrate a mixing model to a target reproduction number", "topics": [ "calibrate_mixing_model" ] }, { "page": "format.measles_parameters", "title": "Format and print the measles parameter table", "topics": [ "format.measles_parameters", "print.measles_parameters" ] }, { "page": "InterventionMeaslesPEP", "title": "Create a measles post-exposure prophylaxis (PEP) intervention", "topics": [ "InterventionMeaslesPEP" ] }, { "page": "make_cmat_symmetric", "title": "Symmetrise a contact matrix based on population sizes", "topics": [ "make_cmat_symmetric" ] }, { "page": "measles_parameters", "title": "Measles model parameters and literature references", "topics": [ "measles_parameters" ] }, { "page": "ModelMeaslesMixing", "title": "Measles model with mixing", "concept": [ "Models", "measles models", "measles-models" ], "topics": [ "epiworld_measlesmixing", "ModelMeaslesMixing" ] }, { "page": "ModelMeaslesMixingRiskQuarantine", "title": "Measles model with mixing and risk-based quarantine", "concept": [ "Models", "measles models", "measles-models" ], "topics": [ "epiworld_measlesmixingriskquarantine", "ModelMeaslesMixingRiskQuarantine" ] }, { "page": "ModelMeaslesSchool", "title": "Measles model with quarantine", "concept": [ "Models", "measles models", "measles-models" ], "topics": [ "epiworld_measlesschool", "ModelMeaslesQuarantine", "ModelMeaslesSchool" ] }, { "page": "short_creek", "title": "Short Creek Population Data by Age Group", "topics": [ "short_creek" ] }, { "page": "short_creek_matrix", "title": "Short Creek Mixing Matrix", "topics": [ "short_creek_matrix" ] } ], "_pkglogo": "https://github.com/UofUEpiBio/measles/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/UofUEpiBio/measles/raw/HEAD/README.md", "_rundeps": [ "cpp11", "epiworldR" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "short-creek.qmd", "filename": "short-creek.html", "title": "Mixing model in Short Creek", "engine": "quarto::html", "headings": [ "How to cite", "Set up", "Creating the model", "Outbreak size", "Hospitalizations", "Scenario without Quarantine", "Final comments" ], "created": "2025-12-18 18:47:28", "modified": "2026-08-06 07:31:30", "commits": 11 }, { "source": "parameters.qmd", "filename": "parameters.html", "title": "Parameters and literature references", "engine": "quarto::html", "headings": [ "How to cite", "The parameter table", "Calibrating to R0", "Hospitalization: rate vs probability", "Inactive parameters", "References" ], "created": "2026-10-09 15:58:29", "modified": "2026-10-09 19:59:26", "commits": 4 }, { "source": "school.qmd", "filename": "school.html", "title": "School-based transmission model", "engine": "quarto::html", "headings": [ "How to cite", "Building the model", "Running the model", "Adding post-exposure prophylaxis (PEP)" ], "created": "2026-04-06 22:47:40", "modified": "2026-08-06 07:31:30", "commits": 5 } ], "_score": 7.515343893088382, "_indexed": true, "_nocasepkg": "measles", "_universes": [ "uofuepibio", "gvegayon" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.4.1-0", "date": "2026-10-09T21:10:18.000Z", "distro": "resolute", "arch": "aarch64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/db4d05228469ceec7dc10cbc5d205fa8a974a9cf741cc2f3942d9aa8c6d54664", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.7.0", "os": "linux", "version": "0.4.1-0", "date": "2026-10-09T21:10:17.000Z", "distro": "resolute", "arch": "x86_64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/15fbdc72442fd8f2bc65f76fa6a70428598bb1cae37c67d5b4a268af2294beab", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.6.1", "os": "linux", "version": "0.4.1-0", "date": "2026-10-09T21:10:22.000Z", "distro": "resolute", "arch": "aarch64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/aeee1346941ee2869ef0762bd657426fd886a54ff2c292a3fbcd44ee5c474afb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.6.1", "os": "linux", "version": "0.4.1-0", "date": "2026-10-09T21:10:15.000Z", "distro": "resolute", "arch": "x86_64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/9943fe54d609866d34378e5332ba2be4348fea7b0144e30ae8123a2603843ecd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.5.3", "os": "mac", "version": "0.4.1-0", "date": "2026-10-09T21:10:55.000Z", "arch": "aarch64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/40185a6eeb8065c604759b8b176614b2a49edd3aa4248c1efa02bde25dd1b06a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.5.3", "os": "mac", "version": "0.4.1-0", "date": "2026-10-09T21:10:53.000Z", "arch": "x86_64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/9b9b9365f1764bc1da5d4d752687719a84776c4d335d543317e3a10157f855ce", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.6.1", "os": "mac", "version": "0.4.1-0", "date": "2026-10-09T21:10:40.000Z", "arch": "aarch64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/48f5d4116a73ff01db3a9b9064ce7eb46173703df772a60a99a314f9564e38a2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.6.1", "os": "mac", "version": "0.4.1-0", "date": "2026-10-09T21:12:09.000Z", "arch": "x86_64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/dfbcf6e366cba4a56aed4281e9f662e4cab888773c7eacdadc90e82bf0a83dec", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.6.0", "os": "wasm", "version": "0.4.1-0", "date": "2026-10-09T21:10:15.000Z", "arch": "emscripten", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/47e68ddca75f98c3671528649168e4e6cfe5ed9b7a7bc17ee451eaa26bc7967d", "status": "success", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.7.0", "os": "win", "version": "0.4.1-0", "date": "2026-10-09T21:12:25.000Z", "arch": "aarch64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/49197f9709d1b2e6be6f35072a1c482820831c65f5650422096b8cd29e7b2702", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.7.0", "os": "win", "version": "0.4.1-0", "date": "2026-10-09T21:10:36.000Z", "arch": "x86_64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/87d0304cf8e75a44f868ce76f70bc14a30d199f146ed46028f9fd69cf5dd7cd3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.5.3", "os": "win", "version": "0.4.1-0", "date": "2026-10-09T21:09:58.000Z", "arch": "x86_64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/cf47252ce35c9776ac7b1bc2eccb0ea993a691129901f70ed91f09cd54de2942", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.6.1", "os": "win", "version": "0.4.1-0", "date": "2026-10-09T21:13:42.000Z", "arch": "aarch64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/5d30168c5adf86922a912da7fa84efef3a61a5c53e1eaaf3d7d8483aec7a97f0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" }, { "r": "4.6.1", "os": "win", "version": "0.4.1-0", "date": "2026-10-09T21:10:55.000Z", "arch": "x86_64", "commit": "d1e87fed204ebe820620759fa1b85cdb9d2e0b03", "fileid": "https://r2.ropensci.org/932c32fd1ce02b089d18b78d88fe629bfe9b94cd78e99e9fcfc6d4cfa9a7be8c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/37991121630" } ] }