{
  "_id": "6ad5c6f343d630dc48a40183",
  "Package": "iDOVE",
  "Type": "Package",
  "Title": "Durability of Vaccine Efficacy Against SARS-CoV-2 Infection",
  "Version": "1.5",
  "Date": "2023-12-13",
  "Authors@R": "c(person(\"Yu\", \"Gu\", role = \"aut\"),\nperson(\"Shannon T.\", \"Holloway\", role = c(\"aut\", \"cre\"),\nemail = \"shannon.t.holloway@gmail.com\"),\nperson(\"Dan-Yu\", \"Lin\", role = \"aut\"))",
  "Author": "Yu Gu [aut], Shannon T. Holloway [aut, cre], Dan-Yu Lin [aut]",
  "Maintainer": "Shannon T. Holloway <shannon.t.holloway@gmail.com>",
  "Description": "Implements a nonparametric maximum likelihood method for\nassessing potentially time-varying vaccine efficacy (VE)\nagainst SARS-CoV-2 infection under staggered enrollment and\ntime-varying community transmission, allowing crossover of\nplacebo volunteers to the vaccine arm. Lin, D. Y., Gu, Y.,\nZeng, D., Janes, H. E., and Gilbert, P. B. (2021)\n<doi:10.1093/cid/ciab630>.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "VignetteBuilder": "utils, knitr",
  "RoxygenNote": "7.2.3",
  "Collate": "'VEplot.R' 'VEcal.R' 'postProcess.R' 'EMmeth.R'\n'RcppExports.R' 'verifyInputs.R' 'idove.R' 'idoveData.R'\n'intCens.R' 'plot.iDOVE.R' 'print.iDOVE.R'",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-19 07:15:41 UTC",
    "User": "root"
  },
  "Repository": "https://sth1402.r-universe.dev",
  "Date/Publication": "2023-12-14 02:38:35 UTC",
  "RemoteUrl": "https://github.com/cran/iDOVE",
  "RemoteRef": "HEAD",
  "RemoteSha": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
  "_user": "sth1402",
  "_type": "src",
  "_file": "iDOVE_1.5.tar.gz",
  "_fileid": "https://r2.ropensci.org/cb8eb752d184355916dab4200795784c1fc4082a86b4ff718ca1cc36f4b8368c",
  "_filesize": 614694,
  "_sha256": "cb8eb752d184355916dab4200795784c1fc4082a86b4ff718ca1cc36f4b8368c",
  "_expires": "2027-01-27T07:29:54.000Z",
  "_created": "2026-10-19T07:15:41.000Z",
  "_published": "2026-10-19T07:29:55.725Z",
  "_buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 117936430017,
      "time": 146,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12169665583"
    },
    {
      "job": 117936430266,
      "time": 169,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12169620419"
    },
    {
      "job": 117936429952,
      "time": 102,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12169287186"
    },
    {
      "job": 117936430600,
      "time": 129,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12168892631"
    },
    {
      "job": 117936430153,
      "time": 167,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12169558218"
    },
    {
      "job": 117936430047,
      "time": 201,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12169402540"
    },
    {
      "job": 117936429908,
      "time": 132,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12169806419"
    },
    {
      "job": 117936430046,
      "time": 277,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12169233470"
    },
    {
      "job": 117935188838,
      "time": 215,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12169355864"
    },
    {
      "job": 117936429933,
      "time": 106,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12169401794"
    },
    {
      "job": 117936430005,
      "time": 239,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12168879217"
    },
    {
      "job": 117936430032,
      "time": 162,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12169715506"
    },
    {
      "job": 117936430042,
      "time": 132,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12168424261"
    },
    {
      "job": 117936430166,
      "time": 225,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12169117034"
    },
    {
      "job": 117936430029,
      "time": 142,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12169670628"
    }
  ],
  "_upstream": "https://github.com/cran/iDOVE",
  "_commit": {
    "id": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
    "author": "Shannon T. Holloway <shannon.t.holloway@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.5\n",
    "time": 1702521515
  },
  "_maintainer": {
    "name": "Shannon T. Holloway",
    "email": "shannon.t.holloway@gmail.com",
    "login": "sth1402",
    "description": "",
    "uuid": 41195707
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.4.6",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "RcppArmadillo",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "sth1402",
      "count": 2,
      "uuid": 41195707
    }
  ],
  "_userbio": {
    "uuid": 41195707,
    "type": "user",
    "name": "sth1402",
    "followers": 1
  },
  "_downloads": {
    "count": 348,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/iDOVE"
  },
  "_mentions": 1,
  "_searchresults": 0,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/iDOVE.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_realowner": "sth1402",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.3",
      "date": "2021-09-15"
    },
    {
      "version": "1.4",
      "date": "2022-06-07"
    },
    {
      "version": "1.5",
      "date": "2023-12-14"
    }
  ],
  "_exports": [
    "idove",
    "intCens"
  ],
  "_datasets": [
    {
      "name": "idoveData",
      "title": "Toy Dataset For Illustration",
      "object": "idoveData",
      "file": "idoveData.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "entry.time",
        "left.time",
        "right.time",
        "vaccine.time",
        "priority",
        "sex"
      ],
      "rows": 40000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "idove",
      "title": "Durability of Vaccine Efficacy Against Asymptomatic SARS-CoV-2 Infection",
      "topics": [
        "idove"
      ]
    },
    {
      "page": "idoveData",
      "title": "Toy Dataset For Illustration",
      "topics": [
        "idoveData"
      ]
    },
    {
      "page": "intCens",
      "title": "Specify Time Variables",
      "topics": [
        "intCens"
      ]
    },
    {
      "page": "plot",
      "title": "Plot Estimated Vaccine Efficacy",
      "topics": [
        "plot",
        "plot.iDOVE"
      ]
    },
    {
      "page": "print",
      "title": "Print the Primary Results of an idove() Analysis",
      "topics": [
        "print",
        "print.iDOVE"
      ]
    }
  ],
  "_rundeps": [
    "Rcpp",
    "RcppArmadillo"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "iDOVE_vignette.Rmd",
      "filename": "iDOVE_vignette.html",
      "title": "iDOVE -- $\\text{\\underline{D}}$urability $\\text{\\underline{O}}$f $\\text{\\underline{V}}$accine $\\text{\\underline{E}}$fficacy Against SARS-CoV-2 $\\text{\\underline{I}}$nfection",
      "author": "Yu Gu, Shannon T. Holloway, and Dan-Yu Lin",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Functions",
        "\\textit",
        "\\textit",
        "\\textit",
        "\\textit",
        "Examples",
        "changePts:",
        "performing nonparametric maximum likelihood",
        "Iteration 100 : difference = 0.000140",
        "EM algorithm converged after 118 iterations",
        "Number of subjects: 40000",
        "Number of unique time points: 313",
        "Log-likelihood at final estimates: -10880.11",
        "PL converged after 2 iterations",
        "constantVE selected",
        "changePts not given; using AIC to select from",
        "evaluating change point: 28",
        "EM algorithm converged after 28 iterations",
        "evaluating change point: 35",
        "EM algorithm converged after 29 iterations",
        "evaluating change point: 42",
        "evaluating change point: 49",
        "EM algorithm converged after 30 iterations",
        "evaluating change point: 56",
        "Day 28 (week 4) was selected as the change point by AIC",
        "Partial log-likelihood at final estimates: -10909.76",
        "PL converged after 1 iterations"
      ],
      "created": "2021-09-15 08:00:05",
      "modified": "2023-12-14 02:38:35",
      "commits": 2
    }
  ],
  "_score": 2,
  "_indexed": true,
  "_nocasepkg": "idove",
  "_universes": [
    "sth1402"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5",
      "date": "2026-10-19T07:18:04.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/4c6062ed471684696d0dd7bd2a9037597b24d20840a48b4fc232270cac3b3a50",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5",
      "date": "2026-10-19T07:18:31.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/e4866fb9b8eb29157585e1c237b51186b1bbf8be8b82bb0960901a2d04bd88c1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.5",
      "date": "2026-10-19T07:17:30.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/54357b0107678a40bcf6857cef721a3b5d005bd7c7bd774d510e08da779a5945",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.5",
      "date": "2026-10-19T07:17:55.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/adff6c0185f0511a4e754b0eb0bc37460c0c3c437a7bcebcc6fcc45a780766e5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5",
      "date": "2026-10-19T07:28:35.000Z",
      "arch": "aarch64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/08ea745872289eb9b81563cdba5151e2d5a6b144217a7d4595ada0af4cfa2edc",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5",
      "date": "2026-10-19T07:20:47.000Z",
      "arch": "x86_64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/e9597c0f7dc75a68a4b4ae8ce609b83776d44d2385cf4dc98be92745c9ae262e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.5",
      "date": "2026-10-19T07:26:12.000Z",
      "arch": "aarch64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/51e36ba9ce3aa9521000e217917412a0ecf87a8c81ea2504c55043f81ce8228d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.5",
      "date": "2026-10-19T07:21:19.000Z",
      "arch": "x86_64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/14b72819838b75c6029feacd98091ca20893030fa16d176f1325975813c4c0f0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.5",
      "date": "2026-10-19T07:17:47.000Z",
      "arch": "emscripten",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/13cb96f1581415b28585070fe3cc41c8d66a6bf66f10a57db9f525853d9ac615",
      "status": "success",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.5",
      "date": "2026-10-19T07:19:17.000Z",
      "arch": "aarch64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/b6a857f66bfd6c03a3459c0359e3c7f2da3b940c3be20b6f9658885692b23ee9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.5",
      "date": "2026-10-19T07:17:08.000Z",
      "arch": "x86_64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/04df32c16bae8ae36443f64baab92082893b72e67873f2d9a5c8fc39bcfc4dfe",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.5",
      "date": "2026-10-19T07:17:06.000Z",
      "arch": "x86_64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/65c069f1b94ef3545177faff30effe865451261d54725a788b5d72604ce24168",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.5",
      "date": "2026-10-19T07:19:06.000Z",
      "arch": "aarch64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/5d9d4d1ad7b4f28c5e3f9cd6fbf9dd1bb3eb9582a48f7c8f63e78447295b2709",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.5",
      "date": "2026-10-19T07:17:15.000Z",
      "arch": "x86_64",
      "commit": "eb9ad765acb01aa62b4e6c98d2c05c1f00823693",
      "fileid": "https://r2.ropensci.org/94b5cad508675a667e04341e12985cfc0daefe84724e29333f4e47296c4e0c0a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/sth1402/actions/runs/39214467753"
    }
  ]
}