{ "_id": "6a1018c0acfb0bcc41c85a8d", "Type": "Package", "Package": "rtestim", "Title": "Estimate the Effective Reproductive Number with Trend Filtering", "Version": "1.0.2.9001", "Authors@R": "c(\nperson(\"Daniel J.\", \"McDonald\", , \"daniel@stat.ubc.ca\", role = c(\"aut\", \"cre\", \"cph\")),\nperson(\"Jiaping\", \"Liu\", , \"jiaping.liu@stat.ubc.ca\", role = \"aut\"),\nperson(\"Zhenglun\", \"Cai\", , \"zhenglun.cai@stat.ubc.ca\", role = \"ctb\")\n)", "Description": "Use trend filtering, a type of regularized nonparametric\nregression, to estimate the instantaneous reproduction number,\nalso called Rt. This value roughly says how many new infections\nwill result from each new infection today. Values larger than\n1 indicate that an epidemic is growing while those less than 1\nindicate decline. For more details about this methodology, see\nLiu, Cai, Gustafson, and McDonald (2024)\n.", "License": "MIT + file LICENSE", "URL": "https://github.com/dajmcdon/rtestim,\nhttps://dajmcdon.github.io/rtestim/", "BugReports": "https://github.com/dajmcdon/rtestim/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/Needs/website": "rmarkdown", "Config/pak/sysreqs": "cmake make libuv1-dev", "Repository": "https://dajmcdon.r-universe.dev", "Date/Publication": "2026-05-14 19:23:37 UTC", "RemoteUrl": "https://github.com/dajmcdon/rtestim", "RemoteRef": "HEAD", "RemoteSha": "fa078efe991c2ed1b90b658e7ec181101665af97", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-14 20:21:51 UTC", "User": "root" }, "Author": "Daniel J. McDonald [aut, cre, cph],\nJiaping Liu [aut],\nZhenglun Cai [ctb]", "Maintainer": "Daniel J. McDonald ", "MD5sum": "353e4b0c17293b5b3868b12e4bc201cd", "_user": "dajmcdon", "_type": "src", "_file": "rtestim_1.0.2.9001.tar.gz", "_fileid": "5870ae2bfa7697add6f7e37acb664215e71da993d01ae864eb2a24cc29287d06", "_filesize": 1627040, "_sha256": "5870ae2bfa7697add6f7e37acb664215e71da993d01ae864eb2a24cc29287d06", "_created": "2026-05-14T20:21:51.000Z", "_published": "2026-05-22T08:50:08.637Z", "_distro": "noble", "_jobs": [ { "job": 77346794974, "time": 190, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7004039805" }, { "job": 77346795186, "time": 189, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7004039460" }, { "job": 77346795278, "time": 191, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7004039967" }, { "job": 77346795353, "time": 205, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7004044158" }, { "job": 77346795384, "time": 133, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7004021713" }, { "job": 77346795235, "time": 334, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7004084039" }, { "job": 77346795090, "time": 140, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7004024654" }, { "job": 77346795059, "time": 222, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7004049290" }, { "job": 77346794666, "time": 251, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7003980370" }, { "job": 77346794497, "time": 154, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7156538904" }, { "job": 77346794712, "time": 251, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7004058157" }, { "job": 77346795286, "time": 169, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7004033273" }, { "job": 77346795101, "time": 196, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7004042258" } ], "_buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/dajmcdon/rtestim", "_commit": { "id": "fa078efe991c2ed1b90b658e7ec181101665af97", "author": "Daniel J. McDonald ", "committer": "Daniel J. McDonald ", "message": "bump version to reflect update.\n", "time": 1778786617 }, "_maintainer": { "name": "Daniel J. McDonald", "email": "daniel@stat.ubc.ca", "login": "dajmcdon", "uuid": 20528078 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.2", "role": "Depends" }, { "package": "BH", "role": "LinkingTo" }, { "package": "dspline", "role": "LinkingTo" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "testthat", "role": "LinkingTo" }, { "package": "tvdenoising", "role": "LinkingTo" }, { "package": "checkmate", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "dspline", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tvdenoising", "role": "Imports" }, { "package": "vctrs", "role": "Imports" }, { "package": "dplyr", "role": "Suggests" }, { "package": "forcats", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "nnet", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "xml2", "role": "Suggests" } ], "_owner": "dajmcdon", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-20", "n": 2 }, { "week": "2025-27", "n": 5 }, { "week": "2025-32", "n": 3 }, { "week": "2025-43", "n": 4 }, { "week": "2026-10", "n": 5 }, { "week": "2026-11", "n": 2 }, { "week": "2026-20", "n": 2 } ], "_tags": [ { "name": "v1.0.0", "date": "2025-07-01" }, { "name": "v1.0.1", "date": "2025-10-24" }, { "name": "v1.0.2", "date": "2026-03-08" } ], "_stars": 8, "_contributors": [ { "user": "dajmcdon", "count": 276, "uuid": 20528078 }, { "user": "jiapivialiu", "count": 84, "uuid": 70077322 }, { "user": "zcaielvis", "count": 7, "uuid": 43735223 } ], "_userbio": { "uuid": 20528078, "type": "user", "name": "Daniel McDonald" }, "_downloads": { "count": 510, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rtestim" }, "_devurl": "https://github.com/dajmcdon/rtestim", "_pkgdown": "https://dajmcdon.github.io/rtestim/", "_searchresults": 38, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/rtestim.html", "manual.pdf" ], "_homeurl": "https://github.com/dajmcdon/rtestim", "_realowner": "dajmcdon", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2025-07-05" }, { "version": "1.0.1", "date": "2025-10-24" }, { "version": "1.0.2", "date": "2026-03-11" } ], "_exports": [ "confband", "configure_rt_admm", "cv_estimate_rt", "delay_calculator", "discretize_gamma", "estimate_rt", "interpolate_rt" ], "_datasets": [ { "name": "cancovid", "title": "Canadian Incident COVID-19 Cases", "object": "cancovid", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "date", "incident_cases" ], "rows": 1253, "table": true, "tojson": true } ], "_help": [ { "page": "cancovid", "title": "Canadian Incident COVID-19 Cases", "topics": [ "cancovid" ] }, { "page": "confband", "title": "Add confidence bands to estimated Rt or incidence curves", "topics": [ "confband" ] }, { "page": "configure_rt_admm", "title": "Rt estimation algorithm configuration", "topics": [ "configure_rt_admm" ] }, { "page": "cv_estimate_rt", "title": "Leave-kth-out cross validation for choosing a optimal parameter lambda", "topics": [ "cv_estimate_rt" ] }, { "page": "delay_calculator", "title": "Calculate the total infectiousness at each observed time point.", "topics": [ "delay_calculator" ] }, { "page": "discretize_gamma", "title": "Compute the discretized density function for gamma distribution", "topics": [ "discretize_gamma" ] }, { "page": "estimate_rt", "title": "Estimate Rt using smoothness-penalized Poisson likelihood", "topics": [ "estimate_rt" ] }, { "page": "fitted.cv_poisson_rt", "title": "Fitted cv_poisson_rt", "topics": [ "fitted.cv_poisson_rt" ] }, { "page": "interpolate_rt", "title": "Interpolate (or extrapolate) Rt estimates to intermediate design points", "topics": [ "interpolate_rt", "interpolate_rt.cv_poisson_rt", "interpolate_rt.poisson_rt" ] }, { "page": "plot.cv_poisson_rt", "title": "Plot cv_poisson_rt", "topics": [ "plot.cv_poisson_rt" ] }, { "page": "plot.poisson_rt", "title": "Plot estimated Rt values from a 'poisson_rt' object", "topics": [ "plot.poisson_rt" ] }, { "page": "plot.rt_confidence_band", "title": "Plot estimated confidence bands for an estimate of Rt", "topics": [ "plot.rt_confidence_band" ] }, { "page": "predict.cv_poisson_rt", "title": "Predict observed data using estimated Rt", "topics": [ "predict.cv_poisson_rt" ] }, { "page": "predict.poisson_rt", "title": "Predict observed data using estimated Rt", "topics": [ "predict.poisson_rt" ] } ], "_pkglogo": "https://github.com/dajmcdon/rtestim/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/dajmcdon/rtestim/raw/HEAD/README.md", "_rundeps": [ "backports", "BH", "brio", "callr", "checkmate", "cli", "cpp11", "crayon", "desc", "diffobj", "dspline", "evaluate", "farver", "fs", "ggplot2", "glue", "gtable", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "pillar", "pkgbuild", "pkgconfig", "pkgload", "praise", "processx", "ps", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "rlang", "rprojroot", "S7", "scales", "testthat", "tibble", "tvdenoising", "utf8", "vctrs", "viridisLite", "waldo", "withr" ], "_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": "rtestim.Rmd", "filename": "rtestim.html", "title": "rtestim Package Vignette", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Example - synthetic dataset", "Quick start", "Cross Validation", "Uneven Reporting Frequency", "Changing degree of difference operator", "Example - Canadian Covid-19 cases", "Approximate confidence bands" ], "created": "2023-07-08 15:49:13", "modified": "2025-08-06 23:08:51", "commits": 11 } ], "_score": 6.327971623623011, "_indexed": true, "_nocasepkg": "rtestim", "_universes": [ "dajmcdon" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.2.9001", "date": "2026-05-14T20:24:54.000Z", "distro": "noble", "arch": "aarch64", "commit": "fa078efe991c2ed1b90b658e7ec181101665af97", "fileid": "3f3d1d7ffe8ed40dc495b4f56028174d8aed25676c46bdcec1801ace1e3c7adc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421" }, { "r": "4.7.0", "os": "linux", "version": "1.0.2.9001", "date": "2026-05-14T20:24:48.000Z", "distro": "noble", "arch": "x86_64", "commit": "fa078efe991c2ed1b90b658e7ec181101665af97", "fileid": "ace63c6abee2c29c3ba62f3004a61a2d678ab472eb9e6b6b5568b9888dca7039", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421" }, { "r": "4.6.0", "os": "linux", "version": "1.0.2.9001", "date": "2026-05-14T20:24:51.000Z", "distro": "noble", "arch": "aarch64", "commit": "fa078efe991c2ed1b90b658e7ec181101665af97", "fileid": "35b0a70450ee5c1b2c047099b717997222739f991c0a38bb121b0dcb94ec6ca7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421" }, { "r": "4.6.0", "os": "linux", "version": "1.0.2.9001", "date": "2026-05-14T20:25:03.000Z", "distro": "noble", "arch": "x86_64", "commit": "fa078efe991c2ed1b90b658e7ec181101665af97", "fileid": "ed15ba8cb8bed0913f2f6bf8b1a62a2b3308e1aadc5913e0c3b59b974c7b3a0e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421" }, { "r": "4.5.3", "os": "mac", "version": "1.0.2.9001", "date": "2026-05-14T20:24:02.000Z", "arch": "aarch64", "commit": "fa078efe991c2ed1b90b658e7ec181101665af97", "fileid": "e5ae7ea2f3466111bbdda06a63d83848b7752c98bb46f937ae27efa0973e2afa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421" }, { "r": "4.5.3", "os": "mac", "version": "1.0.2.9001", "date": "2026-05-14T20:25:57.000Z", "arch": "x86_64", "commit": "fa078efe991c2ed1b90b658e7ec181101665af97", "fileid": "688984d10d2bdea1eb9886c5b94691b38f5aa1b2ac8c8fecc1ac2a1e427de6e0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421" }, { "r": "4.6.0", "os": "mac", "version": "1.0.2.9001", "date": "2026-05-14T20:24:07.000Z", "arch": "aarch64", "commit": "fa078efe991c2ed1b90b658e7ec181101665af97", "fileid": "032e3c9381c5bf3d5562392614011ede7db73d929a6e787e910c162380d06011", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421" }, { "r": "4.6.0", "os": "mac", "version": "1.0.2.9001", "date": "2026-05-14T20:24:54.000Z", "arch": "x86_64", "commit": "fa078efe991c2ed1b90b658e7ec181101665af97", "fileid": "a80c01c45aa9b6dc4721e8890b7308ca710fb46d9863c1c27b22bd8280a88fdf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421" }, { "r": "4.7.0", "os": "win", "version": "1.0.2.9001", "date": "2026-05-14T20:25:13.000Z", "arch": "x86_64", "commit": "fa078efe991c2ed1b90b658e7ec181101665af97", "fileid": "46394923deb3dabb1a3013feec6372f18d4e9d81a2855df25e5fcabf950eaa27", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421" }, { "r": "4.5.3", "os": "win", "version": "1.0.2.9001", "date": "2026-05-14T20:23:45.000Z", "arch": "x86_64", "commit": "fa078efe991c2ed1b90b658e7ec181101665af97", "fileid": "b0b252dc59b40d5232d8dda31aadb6b222dfcbc51c72667e435e9b5399982198", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421" }, { "r": "4.6.0", "os": "win", "version": "1.0.2.9001", "date": "2026-05-14T20:23:51.000Z", "arch": "x86_64", "commit": "fa078efe991c2ed1b90b658e7ec181101665af97", "fileid": "2e2eb2e5ef4294b2b2e9709a10407a16e07426e1e8b05b0c452dcf443b720f0c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.2.9001", "date": "2026-05-22T08:49:25.000Z", "arch": "emscripten", "commit": "fa078efe991c2ed1b90b658e7ec181101665af97", "fileid": "95917cbecfd6db9bcc258a34c3e3057e96a28fe911c8b4fe6a8c187f17e2d6e4", "status": "success", "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/25883331421" } ] }