{
  "_id": "6a154967acfb0bcc41d58625",
  "Package": "bayefdr",
  "Type": "Package",
  "Title": "Bayesian Estimation and Optimisation of Expected False Discovery\nRate",
  "Version": "0.2.0",
  "Date": "2021-09-18",
  "Authors@R": "c(\nperson(\"Alan\", \"O'Callaghan\",\nemail = \"alan.ocallaghan@outlook.com\",\nrole = c(\"aut\", \"cre\")\n),\nperson(\"Catalina\", \"Vallejos\", role = \"aut\")\n)",
  "Description": "Implements the Bayesian FDR control described by Newton et\nal. (2004), <doi:10.1093/biostatistics/5.2.155>. Allows\noptimisation and visualisation of expected error rates based on\ntail posterior probability tests. Based on code written by\nCatalina Vallejos for BASiCS, see Beyond comparisons of means:\nunderstanding changes in gene expression at the single-cell\nlevel Vallejos et al. (2016) <doi:10.1186/s13059-016-0930-3>.",
  "License": "GPL-3",
  "BugReports": "https://github.com/VallejosGroup/bayefdr/issues",
  "RoxygenNote": "7.1.2",
  "Encoding": "UTF-8",
  "Language": "en-gb",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev",
  "Repository": "https://vallejosgroup.r-universe.dev",
  "Date/Publication": "2021-09-29 16:05:02 UTC",
  "RemoteUrl": "https://github.com/vallejosgroup/bayefdr",
  "RemoteRef": "HEAD",
  "RemoteSha": "319682517c8d2f190da703dcb5b4941fb18196e8",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-26 07:15:18 UTC",
    "User": "root"
  },
  "Author": "Alan O'Callaghan [aut, cre],\nCatalina Vallejos [aut]",
  "Maintainer": "Alan O'Callaghan <alan.ocallaghan@outlook.com>",
  "MD5sum": "11dfeb516925c367ac09a06654460fd7",
  "_user": "vallejosgroup",
  "_type": "src",
  "_file": "bayefdr_0.2.0.tar.gz",
  "_fileid": "65a8c58594218f3303398877cd00ae06a36b3cdc5378b78301cc61a59cb5cdcc",
  "_filesize": 138901,
  "_sha256": "65a8c58594218f3303398877cd00ae06a36b3cdc5378b78301cc61a59cb5cdcc",
  "_created": "2026-05-26T07:15:18.000Z",
  "_published": "2026-05-26T07:19:03.306Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77825427878,
      "time": 154,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7211049106"
    },
    {
      "job": 77825427964,
      "time": 131,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211042871"
    },
    {
      "job": 77825428015,
      "time": 191,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7211047311"
    },
    {
      "job": 77825427907,
      "time": 147,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211038587"
    },
    {
      "job": 77825070627,
      "time": 158,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211004175"
    },
    {
      "job": 77825427913,
      "time": 122,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211040345"
    },
    {
      "job": 77825428067,
      "time": 102,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7211037135"
    },
    {
      "job": 77825428196,
      "time": 93,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7211033294"
    },
    {
      "job": 77825427969,
      "time": 84,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211030316"
    }
  ],
  "_buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26437939984",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/vallejosgroup/bayefdr",
  "_commit": {
    "id": "319682517c8d2f190da703dcb5b4941fb18196e8",
    "author": "Alan O'Callaghan <alan.ocallaghan@outlook.com>",
    "committer": "Alan O'Callaghan <alan.ocallaghan@outlook.com>",
    "message": "Retroactive CRAN comments\n",
    "time": 1632931502
  },
  "_maintainer": {
    "name": "Alan OCallaghan",
    "email": "alan.ocallaghan@outlook.com",
    "login": "alanocallaghan",
    "description": "Biomedical data - stats - programming",
    "uuid": 10779688
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "assertthat",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "ggExtra",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "pkgdown",
      "role": "Suggests"
    }
  ],
  "_owner": "vallejosgroup",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "alanocallaghan",
      "count": 39,
      "uuid": 10779688
    },
    {
      "user": "nathansam",
      "count": 2,
      "uuid": 10416927
    }
  ],
  "_userbio": {
    "uuid": 38918233,
    "type": "organization",
    "name": "VallejosGroup"
  },
  "_downloads": {
    "count": 261,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bayefdr"
  },
  "_devurl": "https://github.com/vallejosgroup/bayefdr",
  "_searchresults": 1,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/bayefdr.html",
    "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",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/vallejosgroup/bayefdr",
  "_realowner": "vallejosgroup",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2020-07-30"
    },
    {
      "version": "0.2.0",
      "date": "2021-09-29"
    },
    {
      "version": "0.2.1",
      "date": "2022-10-26"
    }
  ],
  "_exports": [
    "cumplot",
    "efdr",
    "efdr_search",
    "efnr",
    "optimal",
    "traceplot"
  ],
  "_help": [
    {
      "page": "bayefdr-package",
      "title": "The 'nibbles' package.",
      "topics": [
        "bayefdr-package",
        "bayefdr"
      ]
    },
    {
      "page": "cumplot",
      "title": "Plot the cumulative median, mean, and 95% high posterior density region.",
      "topics": [
        "cumplot"
      ]
    },
    {
      "page": "efdr-efnr",
      "title": "EFDR and EFNR estimation",
      "topics": [
        "efdr",
        "efnr"
      ]
    },
    {
      "page": "efdr_search",
      "title": "Bayesian EFDR optimisation.",
      "topics": [
        "efdr_search"
      ]
    },
    {
      "page": "optimal",
      "title": "Retrieve the index of the optimal probability threshold.",
      "topics": [
        "optimal"
      ]
    },
    {
      "page": "plot.bayefdr",
      "title": "Plot the EFDR, EFNR grids of a bayefdr object.",
      "topics": [
        "plot.bayefdr"
      ]
    },
    {
      "page": "utils",
      "title": "Print methods for bayefdr objects.",
      "topics": [
        "head.bayefdr",
        "print.bayefdr"
      ]
    },
    {
      "page": "traceplot",
      "title": "Trace, marginal density histogram, and autocorrelation plot of MCMC draws.",
      "topics": [
        "traceplot"
      ]
    }
  ],
  "_readme": "https://github.com/vallejosgroup/bayefdr/raw/HEAD/README.md",
  "_rundeps": [
    "assertthat",
    "base64enc",
    "bslib",
    "cachem",
    "cli",
    "colourpicker",
    "commonmark",
    "cowplot",
    "cpp11",
    "digest",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "ggExtra",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lifecycle",
    "magrittr",
    "memoise",
    "mime",
    "miniUI",
    "otel",
    "plyr",
    "promises",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "rlang",
    "rmarkdown",
    "S7",
    "sass",
    "scales",
    "shiny",
    "shinyjs",
    "sourcetools",
    "stringi",
    "stringr",
    "tinytex",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "xtable",
    "yaml"
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "bayefdr",
  "_universes": [
    "vallejosgroup",
    "alanocallaghan"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.0",
      "date": "2026-05-26T07:17:45.000Z",
      "distro": "noble",
      "commit": "319682517c8d2f190da703dcb5b4941fb18196e8",
      "fileid": "8582b9ad0abe9f631c4bb5cdc75d7dd0731babc60ddf5cd3df63f8c8881bd859",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26437939984"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.2.0",
      "date": "2026-05-26T07:17:24.000Z",
      "distro": "noble",
      "commit": "319682517c8d2f190da703dcb5b4941fb18196e8",
      "fileid": "fe5b61b0554b29bf31c71ad37dd17f5e8b7b07a3eee52bf9d2eed869570a9546",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26437939984"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.0",
      "date": "2026-05-26T07:17:45.000Z",
      "commit": "319682517c8d2f190da703dcb5b4941fb18196e8",
      "fileid": "899d75e1442033f6196f0e2c1f5c66554da14aa0fa53a66c22399e998415e06b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26437939984"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.2.0",
      "date": "2026-05-26T07:17:14.000Z",
      "commit": "319682517c8d2f190da703dcb5b4941fb18196e8",
      "fileid": "e4003447f00c43525731164422c3ce1d6856951e47f83cc02d777cec6deb1580",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26437939984"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.2.0",
      "date": "2026-05-26T07:17:38.000Z",
      "commit": "319682517c8d2f190da703dcb5b4941fb18196e8",
      "fileid": "1ee9a37350cc12648e807001bdef2e523ce099f9179f5704029a60796202d2da",
      "status": "success",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26437939984"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.0",
      "date": "2026-05-26T07:17:00.000Z",
      "commit": "319682517c8d2f190da703dcb5b4941fb18196e8",
      "fileid": "e1e3a33b9812dafd221d07f9ec313e82a7107f404a21a4f0b2027adf915f9612",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26437939984"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.2.0",
      "date": "2026-05-26T07:16:44.000Z",
      "commit": "319682517c8d2f190da703dcb5b4941fb18196e8",
      "fileid": "ff30ca8f88432f91682eec349e4bf17c19f187b85c689e04dc27e8d157688545",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26437939984"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.2.0",
      "date": "2026-05-26T07:16:32.000Z",
      "commit": "319682517c8d2f190da703dcb5b4941fb18196e8",
      "fileid": "95115d8f9a7a31e19ca1975d622cb66722a566c53c481c0617543508d0dcddd2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vallejosgroup/actions/runs/26437939984"
    }
  ]
}