{
  "_id": "6a548904ff0138dec5d64d52",
  "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<doi:10.1371/journal.pcbi.1012324>.",
  "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": "2026-07-13 06:36:35 UTC",
    "User": "root"
  },
  "Author": "Daniel J. McDonald [aut, cre, cph],\nJiaping Liu [aut],\nZhenglun Cai [ctb]",
  "Maintainer": "Daniel J. McDonald <daniel@stat.ubc.ca>",
  "_user": "dajmcdon",
  "_type": "src",
  "_file": "rtestim_1.0.2.9001.tar.gz",
  "_fileid": "https://r2.ropensci.org/53799be93454613f702577a74ee8dc1025ac1b6fcf9dcee3b3bf6303c3c66004",
  "_filesize": 1629747,
  "_sha256": "53799be93454613f702577a74ee8dc1025ac1b6fcf9dcee3b3bf6303c3c66004",
  "_expires": "2026-10-21T06:43:15.000Z",
  "_created": "2026-07-13T06:36:35.000Z",
  "_published": "2026-07-13T06:43:16.770Z",
  "_jobs": [
    {
      "job": 86750553619,
      "time": 181,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8271034032"
    },
    {
      "job": 86750553613,
      "time": 185,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8271034363"
    },
    {
      "job": 86750553614,
      "time": 226,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8271047004"
    },
    {
      "job": 86750553606,
      "time": 179,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8271032784"
    },
    {
      "job": 86750553605,
      "time": 102,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8271010513"
    },
    {
      "job": 86750553599,
      "time": 338,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8271078467"
    },
    {
      "job": 86750553583,
      "time": 149,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8271024315"
    },
    {
      "job": 86750553630,
      "time": 286,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8271063633"
    },
    {
      "job": 86749899410,
      "time": 263,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8270980866"
    },
    {
      "job": 86750553536,
      "time": 147,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8271023837"
    },
    {
      "job": 86750553576,
      "time": 156,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8271026337"
    },
    {
      "job": 86750553589,
      "time": 151,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8271024610"
    },
    {
      "job": 86750553600,
      "time": 142,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8271022148"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383",
  "_status": "success",
  "_upstream": "https://github.com/dajmcdon/rtestim",
  "_commit": {
    "id": "fa078efe991c2ed1b90b658e7ec181101665af97",
    "author": "Daniel J. McDonald <dajmcdon@gmail.com>",
    "committer": "Daniel J. McDonald <dajmcdon@gmail.com>",
    "message": "bump version to reflect update.\n",
    "time": 1778786617
  },
  "_maintainer": {
    "name": "Daniel J. McDonald",
    "email": "daniel@stat.ubc.ca",
    "login": "dajmcdon",
    "description": "",
    "uuid": 20528078
  },
  "_distro": "resolute",
  "_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": "2025-32",
      "n": 3
    },
    {
      "week": "2025-43",
      "n": 4
    },
    {
      "week": "2026-10",
      "n": 5
    },
    {
      "week": "2026-11",
      "n": 2
    },
    {
      "week": "2026-20",
      "n": 2
    }
  ],
  "_tags": [
    {
      "name": "v1.0.1",
      "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",
    "followers": 60
  },
  "_downloads": {
    "count": 471,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rtestim"
  },
  "_devurl": "https://github.com/dajmcdon/rtestim",
  "_pkgdown": "https://dajmcdon.github.io/rtestim/",
  "_searchresults": 40,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_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",
    "LICENSE",
    "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",
    "otel",
    "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": "16-20260322-1ubuntu1",
      "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": 6.204119982655925,
  "_indexed": true,
  "_nocasepkg": "rtestim",
  "_universes": [
    "dajmcdon"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.2.9001",
      "date": "2026-07-13T06:39:36.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "fa078efe991c2ed1b90b658e7ec181101665af97",
      "fileid": "https://r2.ropensci.org/7e4e265b7da36fe40e5a84e8c7b5118845b206111922a7cf8b97dda2464007ff",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.2.9001",
      "date": "2026-07-13T06:39:29.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "fa078efe991c2ed1b90b658e7ec181101665af97",
      "fileid": "https://r2.ropensci.org/d5760401d89a4cf14afd80c2834da73537a866b3f2715084e2e25482e8940ba8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.2.9001",
      "date": "2026-07-13T06:40:19.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "fa078efe991c2ed1b90b658e7ec181101665af97",
      "fileid": "https://r2.ropensci.org/af5b43b48d159e2435d09db08d8050e3726b8a4310e9d30e848353822d7fae49",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.2.9001",
      "date": "2026-07-13T06:39:25.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "fa078efe991c2ed1b90b658e7ec181101665af97",
      "fileid": "https://r2.ropensci.org/59f320ca87c94c3fbfa964a1c205d582087011a213ed9296b364316aca35035f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.2.9001",
      "date": "2026-07-13T06:38:21.000Z",
      "arch": "aarch64",
      "commit": "fa078efe991c2ed1b90b658e7ec181101665af97",
      "fileid": "https://r2.ropensci.org/44b81ab07474856934cb6f45b4b2e46a2a82b953f8676a08f581e78328779608",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.2.9001",
      "date": "2026-07-13T06:40:30.000Z",
      "arch": "x86_64",
      "commit": "fa078efe991c2ed1b90b658e7ec181101665af97",
      "fileid": "https://r2.ropensci.org/bc5ffd5de04087b843d51d02a4ee8955da012cb0d30825e12e41b6b3884e0c0d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.2.9001",
      "date": "2026-07-13T06:38:59.000Z",
      "arch": "aarch64",
      "commit": "fa078efe991c2ed1b90b658e7ec181101665af97",
      "fileid": "https://r2.ropensci.org/ade01e7811bb96d05571a77c006587ad708378d1fa0d05dfcc396138631129c2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.2.9001",
      "date": "2026-07-13T06:39:57.000Z",
      "arch": "x86_64",
      "commit": "fa078efe991c2ed1b90b658e7ec181101665af97",
      "fileid": "https://r2.ropensci.org/87571ce5fe06fdb35c97183002dcc189c8c9f598b016ce5e03263e1bfd3ab16a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.2.9001",
      "date": "2026-07-13T06:39:22.000Z",
      "arch": "emscripten",
      "commit": "fa078efe991c2ed1b90b658e7ec181101665af97",
      "fileid": "https://r2.ropensci.org/e81f8366647c5726bd74aa92df108acfbd4702a956deb0f2ea0b428dfd5fc558",
      "status": "success",
      "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.2.9001",
      "date": "2026-07-13T06:38:32.000Z",
      "arch": "x86_64",
      "commit": "fa078efe991c2ed1b90b658e7ec181101665af97",
      "fileid": "https://r2.ropensci.org/a45ebbf5d9a1d794b44eb4ef77687dde8c71f9db48d57ff52a6bd8e6af81bfe1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.2.9001",
      "date": "2026-07-13T06:38:23.000Z",
      "arch": "x86_64",
      "commit": "fa078efe991c2ed1b90b658e7ec181101665af97",
      "fileid": "https://r2.ropensci.org/4db980eda402c6354bd4f7d28552f1fff333399734041453539617bad176c876",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.2.9001",
      "date": "2026-07-13T06:38:19.000Z",
      "arch": "x86_64",
      "commit": "fa078efe991c2ed1b90b658e7ec181101665af97",
      "fileid": "https://r2.ropensci.org/f900a966cadd551a14d559bd81def8895b24bbdba945afb6251eb30c403c49e5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/dajmcdon/actions/runs/29229299383"
    }
  ]
}