{ "_id": "6a2271adcd65a98ecbd4926e", "Package": "measles", "Type": "Package", "Title": "Measles Epidemiological Models", "Version": "0.3.1-0", "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", "Remotes": [ "UofUEpiBio/epiworldR" ], "Repository": "https://uofuepibio.r-universe.dev", "Date/Publication": "2026-04-24 20:37:27 UTC", "RemoteUrl": "https://github.com/UofUEpiBio/measles", "RemoteRef": "HEAD", "RemoteSha": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-05 06:44:02 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 ", "MD5sum": "6dafd60830045e3dac418faced6a169b", "_user": "uofuepibio", "_type": "src", "_file": "measles_0.3.1-0.tar.gz", "_fileid": "0c1b62601dbc477ed8571ee6f0ef8cef2bf76098dafc1f8f1da45ece82e009b7", "_filesize": 1745524, "_sha256": "0c1b62601dbc477ed8571ee6f0ef8cef2bf76098dafc1f8f1da45ece82e009b7", "_created": "2026-06-05T06:44:02.000Z", "_published": "2026-06-05T06:50:21.576Z", "_distro": "noble", "_jobs": [ { "job": 79677910813, "time": 155, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7430498637" }, { "job": 79677910764, "time": 134, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7430493032" }, { "job": 79677910775, "time": 152, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7430498056" }, { "job": 79677910786, "time": 146, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7430495840" }, { "job": 79677910817, "time": 147, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7430496152" }, { "job": 79677910833, "time": 282, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7430526872" }, { "job": 79677910785, "time": 201, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7430508405" }, { "job": 79677910897, "time": 332, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7430539376" }, { "job": 79677317069, "time": 288, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7430460353" }, { "job": 79677910767, "time": 106, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7430486340" }, { "job": 79677910776, "time": 159, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7430498600" }, { "job": 79677910795, "time": 161, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7430499696" }, { "job": 79677910769, "time": 181, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7430504168" } ], "_buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/UofUEpiBio/measles", "_commit": { "id": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "author": "George G. Vega Yon ", "committer": "GitHub ", "message": "Updating the vignette and patching to 0.3.1 (#45)\n\nThis pull request updates the `measles` package to version 0.3.1-0 and introduces several improvements and clarifications to the codebase, documentation, and vignettes. The most notable changes include a bug fix in the quarantine process logic, clarification of model calibration methodology, and the addition of a new scenario in the vignette to compare outcomes with and without quarantine.\n\n**Bug fix:**\n\n* Corrected the quarantine process logic in `_quarantine_process` of `measlesmixing.hpp` by fixing the parenthesis placement in the `within_days` calculation, ensuring proper evaluation of the contact tracing window.\n\n**Documentation and vignette improvements:**\n\n* Clarified the calibration process in the Short Creek vignette, specifying that the scaling factor can be applied to either the transmission probability or the contact matrix, and added a callout warning about the epidemiological implications of each approach.\n* Updated the vignette to include a new scenario that disables quarantine (by setting \"Quarantine period\" to -1), allowing users to compare outbreak sizes with and without quarantine.\n\n**Testing and calibration consistency:**\n\n* Updated model calibration in both the vignette and the `test-calibration.R` unit test to apply the scaling factor to the `transmission_rate` instead of the contact matrix, ensuring consistency with the clarified methodology. [[1]](diffhunk://#diff-211bb3baf148e47aa73263d26cd6dff6b62530a492b12ba9b89d6d1805ba9459L103-R109) [[2]](diffhunk://#diff-e2c3b2544f9b4e742d25a9a71a871f529e97772ab8e548863acb9b1920a3f9fbL38-R40)\n\n**Versioning and release notes:**\n\n* Incremented the package version to 0.3.1-0 in `DESCRIPTION` and updated version macros in `measles.hpp`. Added a new section in `NEWS.md` for this release. [[1]](diffhunk://#diff-9cc358405149db607ff830a16f0b4b21f7366e3c99ec00d52800acebe21b231cL4-R4) [[2]](diffhunk://#diff-60ba74103447c8b40f131ff275114745a8addfd9d7aa989ca659793a", "time": 1777063047 }, "_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" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "epiworldR", "version": ">= 0.14.99.99", "role": "Depends" }, { "package": "cpp11", "role": "LinkingTo" }, { "package": "epiworldR", "version": ">= 0.14.99.99", "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": 0, "_updates": [ { "week": "2025-24", "n": 1 }, { "week": "2025-30", "n": 1 }, { "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 } ], "_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": 2, "_contributors": [ { "user": "gvegayon", "count": 260, "uuid": 893619 }, { "user": "derekmeyer37", "count": 123, "uuid": 105825983 }, { "user": "apulsipher", "count": 25, "uuid": 45372570 }, { "user": "copilot", "count": 13, "uuid": 198982749 }, { "user": "abinashbunty", "count": 1, "uuid": 25522048 } ], "_userbio": { "uuid": 89941410, "type": "organization", "name": "Divisions of Epidemiology and Biostatistics at the U" }, "_downloads": { "count": 472, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/measles" }, "_devurl": "https://github.com/uofuepibio/measles", "_searchresults": 10, "_quarto": true, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/measles.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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", "get_contact_matrix", "InterventionMeaslesPEP", "measles_cpp_version", "ModelMeaslesMixing", "ModelMeaslesMixingRiskQuarantine", "ModelMeaslesQuarantine", "ModelMeaslesSchool", "set_contact_matrix" ], "_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": "contact_matrix", "title": "Get and Set Contact Matrix", "topics": [ "contact_matrix", "get_contact_matrix", "get_contact_matrix.default", "get_contact_matrix.epiworld_measlesmixing", "get_contact_matrix.epiworld_measlesmixingriskquarantine", "set_contact_matrix", "set_contact_matrix.default", "set_contact_matrix.epiworld_measlesmixing", "set_contact_matrix.epiworld_measlesmixingriskquarantine" ] }, { "page": "InterventionMeaslesPEP", "title": "Create a measles post-exposure prophylaxis (PEP) intervention", "topics": [ "InterventionMeaslesPEP" ] }, { "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": "14.2.0-4ubuntu2~24.04.1", "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": [], "created": "2025-12-18 18:47:28", "modified": "2026-04-24 20:37:27", "commits": 9 }, { "source": "school.qmd", "filename": "school.html", "title": "School-based transmission model", "engine": "quarto::html", "headings": [], "created": "2026-04-06 22:47:40", "modified": "2026-04-21 02:10:43", "commits": 4 } ], "_score": 6.204119982655925, "_indexed": true, "_nocasepkg": "measles", "_universes": [ "uofuepibio", "gvegayon" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.1-0", "date": "2026-06-05T06:46:32.000Z", "distro": "noble", "arch": "aarch64", "commit": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "fileid": "8e8fc94c4c194ca287b82b89a411b896e847d908d9741f4869d159462214ebef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562" }, { "r": "4.7.0", "os": "linux", "version": "0.3.1-0", "date": "2026-06-05T06:46:13.000Z", "distro": "noble", "arch": "x86_64", "commit": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "fileid": "09cf63fc2b0d32aa94b64dcb92dbd2d6a43d8a120afeaa167fbb917519c6e8f4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562" }, { "r": "4.6.0", "os": "linux", "version": "0.3.1-0", "date": "2026-06-05T06:46:31.000Z", "distro": "noble", "arch": "aarch64", "commit": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "fileid": "18167058e0844e477a4a7c26d9293aa67f886f313aec9e3bbbd668c67f59c5fd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562" }, { "r": "4.6.0", "os": "linux", "version": "0.3.1-0", "date": "2026-06-05T06:46:18.000Z", "distro": "noble", "arch": "x86_64", "commit": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "fileid": "43525d05c220ea5ff1efaaf114e65633f8ceadda0734f7f691fb1e01d8077394", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562" }, { "r": "4.5.3", "os": "mac", "version": "0.3.1-0", "date": "2026-06-05T06:46:18.000Z", "arch": "aarch64", "commit": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "fileid": "460e9ee1fd09c4e478b108eebff59c326acb58e0503e26431127c5cddc6174f1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562" }, { "r": "4.5.3", "os": "mac", "version": "0.3.1-0", "date": "2026-06-05T06:47:38.000Z", "arch": "x86_64", "commit": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "fileid": "ef18ddf0de884f9937c0960f9cb2a9393dc4c31e8748d2a88b26ae0c9ca4fe5e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562" }, { "r": "4.6.0", "os": "mac", "version": "0.3.1-0", "date": "2026-06-05T06:46:55.000Z", "arch": "aarch64", "commit": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "fileid": "1a328b4032188250dffe4d2cd070e43ad66bb41233d70c455a20fa022ec9faae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562" }, { "r": "4.6.0", "os": "mac", "version": "0.3.1-0", "date": "2026-06-05T06:47:57.000Z", "arch": "x86_64", "commit": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "fileid": "25065cc7a9695e4b2ae30fb2c38a2c775eb1af7fa1760b77e1932e624188cb53", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.1-0", "date": "2026-06-05T06:46:07.000Z", "arch": "emscripten", "commit": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "fileid": "beea8ce69415565012f82f332cb95d872ab5add156cd4a2844de20e42344c202", "status": "success", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562" }, { "r": "4.7.0", "os": "win", "version": "0.3.1-0", "date": "2026-06-05T06:45:53.000Z", "arch": "x86_64", "commit": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "fileid": "70718b70a0af8f8fe8a81b756f357b98adfdc1f90651ec448d7d1575312781eb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562" }, { "r": "4.5.3", "os": "win", "version": "0.3.1-0", "date": "2026-06-05T06:45:53.000Z", "arch": "x86_64", "commit": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "fileid": "76664fd8b5ce85d2bed344d7499584eeb4b40a258bb0a84099315fd933e1303d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562" }, { "r": "4.6.0", "os": "win", "version": "0.3.1-0", "date": "2026-06-05T06:46:07.000Z", "arch": "x86_64", "commit": "8b6d10f20cc07597df10ceb6a58f596ce41817b8", "fileid": "5def99a64ef22409f3212752b0e8aef32cde420daf1539b1a1297555c83193e7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/uofuepibio/actions/runs/26999749562" } ] }