{
  "_id": "6a2268bbcd65a98ecbd458e4",
  "Package": "dcifer",
  "Type": "Package",
  "Title": "Genetic Relatedness Between Polyclonal Infections",
  "Version": "1.5.2",
  "Authors@R": "person(\"Inna\", \"Gerlovina\",\nrole = c(\"aut\", \"cre\"),\nemail = \"innager@berkeley.edu\",\ncomment = c(ORCID = \"0000-0002-7772-7473\"))",
  "Description": "An implementation of Dcifer (Distance for complex\ninfections: fast estimation of relatedness), an identity by\ndescent (IBD) based method to calculate genetic relatedness\nbetween polyclonal infections from biallelic and multiallelic\ndata. The package includes functions that format and preprocess\nthe data, implement the method, and visualize the results.\nGerlovina et al. (2022) <doi:10.1093/genetics/iyac126>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.2",
  "Roxygen": "list(markdown = TRUE)",
  "URL": "https://github.com/EPPIcenter/dcifer,\nhttps://eppicenter.github.io/dcifer/",
  "VignetteBuilder": "knitr",
  "Repository": "https://plasmogenepi.r-universe.dev",
  "Date/Publication": "2026-05-06 22:29:47 UTC",
  "RemoteUrl": "https://github.com/eppicenter/dcifer",
  "RemoteRef": "HEAD",
  "RemoteSha": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-05 06:06:16 UTC",
    "User": "root"
  },
  "Author": "Inna Gerlovina [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-7772-7473>)",
  "Maintainer": "Inna Gerlovina <innager@berkeley.edu>",
  "MD5sum": "4d1681aa05dba56269dc30fa970ad4cd",
  "_user": "plasmogenepi",
  "_type": "src",
  "_file": "dcifer_1.5.2.tar.gz",
  "_fileid": "ad1ec044d9e20bbbe7f4eff1eda383c2006180b7f5e58a972bd07c53b74de6cc",
  "_filesize": 834545,
  "_sha256": "ad1ec044d9e20bbbe7f4eff1eda383c2006180b7f5e58a972bd07c53b74de6cc",
  "_created": "2026-06-05T06:06:16.000Z",
  "_published": "2026-06-05T06:12:10.956Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79673535090,
      "time": 133,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7429966721"
    },
    {
      "job": 79673535097,
      "time": 115,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7429962770"
    },
    {
      "job": 79673535163,
      "time": 128,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7429965801"
    },
    {
      "job": 79673535094,
      "time": 112,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7429962004"
    },
    {
      "job": 79673535092,
      "time": 90,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7429957157"
    },
    {
      "job": 79673535072,
      "time": 217,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7429984966"
    },
    {
      "job": 79673535099,
      "time": 113,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7429962087"
    },
    {
      "job": 79673535061,
      "time": 204,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7429981728"
    },
    {
      "job": 79673274389,
      "time": 139,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7429935879"
    },
    {
      "job": 79673535346,
      "time": 98,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7429958742"
    },
    {
      "job": 79673535075,
      "time": 108,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7429960970"
    },
    {
      "job": 79673535073,
      "time": 103,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7429960152"
    },
    {
      "job": 79673535076,
      "time": 97,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7429959127"
    }
  ],
  "_buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/eppicenter/dcifer",
  "_commit": {
    "id": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
    "author": "innager <innager@berkeley.edu>",
    "committer": "innager <innager@berkeley.edu>",
    "message": "missing data: NA pval, confreg\n",
    "time": 1778106587
  },
  "_maintainer": {
    "name": "Inna Gerlovina",
    "email": "innager@berkeley.edu",
    "login": "innager",
    "description": "",
    "uuid": 12566170,
    "orcid": "0000-0002-7772-7473"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "eppicenter",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-39",
      "n": 1
    },
    {
      "week": "2025-43",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 1
    },
    {
      "week": "2025-45",
      "n": 7
    },
    {
      "week": "2025-46",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 1
    },
    {
      "week": "2026-19",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "v1.3.1",
      "date": "2025-10-27"
    },
    {
      "name": "v1.4.0",
      "date": "2025-11-05"
    },
    {
      "name": "v1.5.0",
      "date": "2025-11-16"
    },
    {
      "name": "v1.5.2",
      "date": "2026-05-06"
    }
  ],
  "_stars": 8,
  "_contributors": [
    {
      "user": "innager",
      "count": 90,
      "uuid": 12566170
    }
  ],
  "_userbio": {
    "uuid": 140542976,
    "type": "organization",
    "name": "PlasmoGenEpi",
    "description": "We are a network of scientists who have come together since 2018 to address challenges in malaria genomic epidemiology."
  },
  "_downloads": {
    "count": 303,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/dcifer"
  },
  "_devurl": "https://github.com/eppicenter/dcifer",
  "_pkgdown": "https://eppicenter.github.io/dcifer/",
  "_searchresults": 25,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/dcifer.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/eppicenter/dcifer",
  "_realowner": "eppicenter",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.1",
      "date": "2022-07-15"
    },
    {
      "version": "1.1.0",
      "date": "2022-08-06"
    },
    {
      "version": "1.1.1",
      "date": "2022-08-10"
    },
    {
      "version": "1.2.0",
      "date": "2022-10-31"
    },
    {
      "version": "1.2.1",
      "date": "2023-12-12"
    },
    {
      "version": "1.5.0",
      "date": "2025-11-11"
    },
    {
      "version": "1.5.2",
      "date": "2026-05-07"
    }
  ],
  "_exports": [
    "calcAfreq",
    "formatAfreq",
    "formatDat",
    "generateReval",
    "getCOI",
    "ibdDat",
    "ibdEstM",
    "ibdPair",
    "logReval",
    "matchAfreq",
    "mixMat",
    "plotColorbar",
    "plotRel",
    "probUxUy",
    "readAfreq",
    "readDat"
  ],
  "_datasets": [
    {
      "name": "dres",
      "title": "Dcifer results",
      "object": "dres",
      "class": [
        "array"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "dsmp",
      "title": "Sample data",
      "object": "dsmp",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "revals",
      "title": "Parameter grid",
      "object": "revals",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calcAfreq",
      "title": "Calculate Allele Frequencies",
      "topics": [
        "calcAfreq"
      ]
    },
    {
      "page": "dres",
      "title": "Dcifer results",
      "topics": [
        "dres"
      ]
    },
    {
      "page": "dsmp",
      "title": "Sample data",
      "topics": [
        "dsmp"
      ]
    },
    {
      "page": "format",
      "title": "Read and Reformat Data",
      "topics": [
        "format",
        "formatAfreq",
        "formatDat",
        "readAfreq",
        "readDat"
      ]
    },
    {
      "page": "generateReval",
      "title": "Grid of Parameter Values",
      "topics": [
        "generateReval"
      ]
    },
    {
      "page": "getCOI",
      "title": "Calculate COI",
      "topics": [
        "getCOI"
      ]
    },
    {
      "page": "IBDdat",
      "title": "Pairwise Relatedness",
      "topics": [
        "ibdDat"
      ]
    },
    {
      "page": "ibdEstM",
      "title": "Estimate Relatedness and a Number of Related Strains",
      "topics": [
        "ibdEstM"
      ]
    },
    {
      "page": "IBDpair",
      "title": "Relatedness Between Two Samples",
      "topics": [
        "ibdPair"
      ]
    },
    {
      "page": "logReval",
      "title": "Logarithms of 'reval'",
      "topics": [
        "logReval"
      ]
    },
    {
      "page": "matchAfreq",
      "title": "Match Samples and Allele Frequencies",
      "topics": [
        "matchAfreq"
      ]
    },
    {
      "page": "mixMat",
      "title": "Combine two matrices",
      "topics": [
        "mixMat"
      ]
    },
    {
      "page": "plotColorbar",
      "title": "Colorbar",
      "topics": [
        "plotColorbar"
      ]
    },
    {
      "page": "plotRel",
      "title": "Plot Relatedness Estimates",
      "topics": [
        "plotRel"
      ]
    },
    {
      "page": "probUxUy",
      "title": "Likelihood for U_x, U_y",
      "topics": [
        "probUxUy"
      ]
    },
    {
      "page": "revals",
      "title": "Parameter grid",
      "topics": [
        "revals"
      ]
    }
  ],
  "_pkglogo": "https://github.com/eppicenter/dcifer/raw/HEAD/man/figures/logo.svg",
  "_readme": "https://github.com/eppicenter/dcifer/raw/HEAD/README.md",
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "vignetteDcifer.Rmd",
      "filename": "vignetteDcifer.html",
      "title": "Dcifer: Genetic Distance Between Polyclonal Infections",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Read and reformat data, estimate COI and population allele frequencies",
        "Estimate relatedness",
        "Visualize the results",
        "Further analysis of related samples"
      ],
      "created": "2022-06-05 06:05:52",
      "modified": "2025-11-07 08:28:21",
      "commits": 11
    }
  ],
  "_score": 5.845098040014257,
  "_indexed": false,
  "_nocasepkg": "dcifer",
  "_universes": [
    "plasmogenepi"
  ],
  "_indexurl": "https://eppicenter.r-universe.dev/dcifer",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5.2",
      "date": "2026-06-05T06:08:35.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
      "fileid": "114375b2556c9e569db27c78b4fe7432b5722db7a9b1e880a3396777be14b7a7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5.2",
      "date": "2026-06-05T06:08:11.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
      "fileid": "b024ad65b7bd3746e82d835da6307a336ea72375d5fc218d05a3c794204943f6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.5.2",
      "date": "2026-06-05T06:08:30.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
      "fileid": "8c17a2f54586bb34e8554f5063c206134ab8bdab822b47ffd68af8f048026e65",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.5.2",
      "date": "2026-06-05T06:08:09.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
      "fileid": "38704b425b8e49d98881c3c6f83244ad2e1b105810b4aef1de03059c1eb7a1b1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5.2",
      "date": "2026-06-05T06:07:48.000Z",
      "arch": "aarch64",
      "commit": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
      "fileid": "47e89b965d73ff36c2ea468da65333fe87b775cb139b35873beff00943f402cb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5.2",
      "date": "2026-06-05T06:08:58.000Z",
      "arch": "x86_64",
      "commit": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
      "fileid": "81de117c1b644c3f6e87fd2686812801ecf1af714656104884227f021ecf5e4f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.5.2",
      "date": "2026-06-05T06:08:03.000Z",
      "arch": "aarch64",
      "commit": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
      "fileid": "f3cac1aad7412ca9096e1a5f9bf897dc7500064f45de1da2f418ca7c421d05f9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.5.2",
      "date": "2026-06-05T06:09:25.000Z",
      "arch": "x86_64",
      "commit": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
      "fileid": "40951979f37f9dbecac11d3cdda1cff84e0639307b0fbfe0e274deff301207fc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.5.2",
      "date": "2026-06-05T06:08:09.000Z",
      "arch": "emscripten",
      "commit": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
      "fileid": "aaf41edbbdf9d7692ed3b49edd36cf8a259011fe386e3f5bf0737d4b9de2d1da",
      "status": "success",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.5.2",
      "date": "2026-06-05T06:07:44.000Z",
      "arch": "x86_64",
      "commit": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
      "fileid": "e9e84041eff4df8469ec54fd3317c23c6e0c359292cf4397518858e83a652eef",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.5.2",
      "date": "2026-06-05T06:07:33.000Z",
      "arch": "x86_64",
      "commit": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
      "fileid": "753bb6b1e9bce21c74458a5d60381d2560096a7dffa2bca5aa8fdd0e66484278",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.5.2",
      "date": "2026-06-05T06:07:38.000Z",
      "arch": "x86_64",
      "commit": "b6255509bba4e96e2f6af1dd033a7ac45e1b2684",
      "fileid": "d6966849eee5488df59f07cbb367cce3677c61eb6ffb28f5d816a14bc8241059",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26998482665"
    }
  ]
}