{
  "_id": "6a2722e324555f66ed528f1a",
  "Package": "malaviR",
  "Type": "Package",
  "Title": "An R interface to MalAvi",
  "Version": "1.0.0",
  "Authors@R": "c(\nperson(\"Vincenzo A\", \"Ellis\", email = \"vaellis@udel.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Staffan\", \"Bensch\", email = \"staffan.bensch@biol.lu.se\", role = \"aut\"),\nperson(\"Bjorn\", \"Canback\", email = \"bjorn.canback@biol.lu.se\", role = \"aut\"))",
  "Maintainer": "Vincenzo A. Ellis <vaellis@udel.edu>",
  "Description": "Functions for working with data from the MalAvi database\nof avian haemosporidian parasites.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.1",
  "URL": "https://github.com/vincenzoaellis/malaviR",
  "BugReports": "https://github.com/vincenzoaellis/malaviR/issues",
  "Repository": "https://vincenzoaellis.r-universe.dev",
  "Date/Publication": "2026-06-08 16:28:36 UTC",
  "RemoteUrl": "https://github.com/vincenzoaellis/malaviR",
  "RemoteRef": "HEAD",
  "RemoteSha": "b9d3de84d102a6ba5c58cf7f1fb3986ad5173051",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-08 20:11:04 UTC",
    "User": "root"
  },
  "Author": "Vincenzo A Ellis [aut, cre],\nStaffan Bensch [aut],\nBjorn Canback [aut]",
  "MD5sum": "e13b3d671b2188ea13a375567d5da93f",
  "_user": "vincenzoaellis",
  "_type": "src",
  "_file": "malaviR_1.0.0.tar.gz",
  "_fileid": "f00d6f3976824e0e14229056b14d2cc7a4e93afde8abb3a0998631172260d716",
  "_filesize": 2230026,
  "_sha256": "f00d6f3976824e0e14229056b14d2cc7a4e93afde8abb3a0998631172260d716",
  "_created": "2026-06-08T20:11:04.000Z",
  "_published": "2026-06-08T20:15:31.823Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 80186502447,
      "time": 234,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7491324592"
    },
    {
      "job": 80186502464,
      "time": 188,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7491308558"
    },
    {
      "job": 80186502449,
      "time": 155,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7491296367"
    },
    {
      "job": 80186502450,
      "time": 196,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7491311177"
    },
    {
      "job": 80185855511,
      "time": 209,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7491239860"
    },
    {
      "job": 80186502442,
      "time": 125,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7491285377"
    },
    {
      "job": 80186502444,
      "time": 190,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7491308890"
    },
    {
      "job": 80186502482,
      "time": 179,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7491305313"
    },
    {
      "job": 80186502470,
      "time": 189,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7491308223"
    }
  ],
  "_buildurl": "https://github.com/r-universe/vincenzoaellis/actions/runs/27163830209",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/vincenzoaellis/malaviR",
  "_commit": {
    "id": "b9d3de84d102a6ba5c58cf7f1fb3986ad5173051",
    "author": "Vincenzo A. Ellis <vaellis@udel.edu>",
    "committer": "Vincenzo A. Ellis <vaellis@udel.edu>",
    "message": "Add r-universe downloads badge to README\n",
    "time": 1780936116
  },
  "_maintainer": {
    "name": "Vincenzo A. Ellis",
    "email": "vaellis@udel.edu",
    "login": "vincenzoaellis",
    "description": "",
    "uuid": 29842250
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Suggests"
    },
    {
      "package": "clootl",
      "role": "Suggests"
    },
    {
      "package": "DECIPHER",
      "version": ">= 3.0",
      "role": "Suggests"
    },
    {
      "package": "readxl",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "vincenzoaellis",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-23",
      "n": 8
    },
    {
      "week": "2026-24",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "vincenzoaellis",
      "count": 70,
      "uuid": 29842250
    }
  ],
  "_userbio": {
    "uuid": 29842250,
    "type": "user",
    "name": "vincenzoaellis"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/malaviR"
  },
  "_devurl": "https://github.com/vincenzoaellis/malavir",
  "_searchresults": 3,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/malaviR.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "blast_malavi",
    "clean_alignment",
    "clean_names",
    "clootl_taxonomy_version",
    "extract_alignment",
    "extract_table",
    "malavi_version",
    "match_taxonomy",
    "sister_taxa",
    "synonymy_report"
  ],
  "_datasets": [
    {
      "name": "taxonomy",
      "title": "MalAvi host species matched to the clootl (eBird) taxonomy",
      "object": "taxonomy",
      "class": [
        "data.frame"
      ],
      "fields": [
        "malavi_species",
        "ebird_species",
        "ott_name",
        "order",
        "family",
        "match_type"
      ],
      "rows": 2339,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "blast_malavi",
      "title": "BLAST-like search of a sequence against MalAvi",
      "topics": [
        "blast_malavi"
      ]
    },
    {
      "page": "clean_alignment",
      "title": "Identify and collapse repeated haplotypes in a MalAvi alignment",
      "topics": [
        "clean_alignment"
      ]
    },
    {
      "page": "clean_names",
      "title": "Clean MalAvi lineage names to match the tables",
      "topics": [
        "clean_names"
      ]
    },
    {
      "page": "clootl_taxonomy_version",
      "title": "Version of the clootl taxonomy bundled in the package",
      "topics": [
        "clootl_taxonomy_version"
      ]
    },
    {
      "page": "extract_alignment",
      "title": "Get the MalAvi sequence alignment",
      "topics": [
        "extract_alignment"
      ]
    },
    {
      "page": "extract_table",
      "title": "Get a MalAvi data table",
      "topics": [
        "extract_table"
      ]
    },
    {
      "page": "malavi_version",
      "title": "MalAvi database version bundled in the package",
      "topics": [
        "malavi_version"
      ]
    },
    {
      "page": "match_taxonomy",
      "title": "Match host species names to the clootl (eBird) avian taxonomy",
      "topics": [
        "match_taxonomy"
      ]
    },
    {
      "page": "sister_taxa",
      "title": "Identify the sister taxa at a node in a phylogeny",
      "topics": [
        "sister_taxa"
      ]
    },
    {
      "page": "synonymy_report",
      "title": "Quantify MalAvi haplotype synonymies for investigation",
      "topics": [
        "synonymy_report"
      ]
    },
    {
      "page": "taxonomy",
      "title": "MalAvi host species matched to the clootl (eBird) taxonomy",
      "topics": [
        "taxonomy"
      ]
    }
  ],
  "_readme": "https://github.com/vincenzoaellis/malaviR/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "cli",
    "digest",
    "dplyr",
    "generics",
    "glue",
    "lattice",
    "lifecycle",
    "magrittr",
    "nlme",
    "pillar",
    "pkgconfig",
    "R6",
    "Rcpp",
    "rlang",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr"
  ],
  "_score": 2,
  "_indexed": true,
  "_nocasepkg": "malavir",
  "_universes": [
    "vincenzoaellis"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-06-08T20:13:14.000Z",
      "distro": "noble",
      "commit": "b9d3de84d102a6ba5c58cf7f1fb3986ad5173051",
      "fileid": "f4a2a4c0be034643cbbca6b55f31178f9d6367a5c41d4e85b22f3f9edd875a59",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vincenzoaellis/actions/runs/27163830209"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-06-08T20:12:56.000Z",
      "distro": "noble",
      "commit": "b9d3de84d102a6ba5c58cf7f1fb3986ad5173051",
      "fileid": "302b40436df06e2405167738ab8f101dd5053f6e9bab52ee018af8f2f755e733",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vincenzoaellis/actions/runs/27163830209"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-06-08T20:12:30.000Z",
      "commit": "b9d3de84d102a6ba5c58cf7f1fb3986ad5173051",
      "fileid": "c83eebc11fca1379b1915d1512ae6edaf40006e36824a6238cd2a44ddf69da25",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vincenzoaellis/actions/runs/27163830209"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-06-08T20:12:58.000Z",
      "commit": "b9d3de84d102a6ba5c58cf7f1fb3986ad5173051",
      "fileid": "79adf890a552f6353cb465ee548dca966bf67c715b978754b2539af157158974",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vincenzoaellis/actions/runs/27163830209"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0",
      "date": "2026-06-08T20:13:25.000Z",
      "commit": "b9d3de84d102a6ba5c58cf7f1fb3986ad5173051",
      "fileid": "bfdb1c3a88c0ba240e13b69ca2e2e505905eecda2910af61a7552d323480ca15",
      "status": "success",
      "buildurl": "https://github.com/r-universe/vincenzoaellis/actions/runs/27163830209"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-06-08T20:12:36.000Z",
      "commit": "b9d3de84d102a6ba5c58cf7f1fb3986ad5173051",
      "fileid": "d8f4ccc51a1cfe4f81a836d3f7c76218105f2c73e9b5d8b953d7e4555e6e5583",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vincenzoaellis/actions/runs/27163830209"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-06-08T20:12:20.000Z",
      "commit": "b9d3de84d102a6ba5c58cf7f1fb3986ad5173051",
      "fileid": "9fd0e375d74fdb0ae123ee5dc54e5b8a184ffa8390bb7b16914237f87ed6b9e9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vincenzoaellis/actions/runs/27163830209"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-06-08T20:12:25.000Z",
      "commit": "b9d3de84d102a6ba5c58cf7f1fb3986ad5173051",
      "fileid": "0bf0703e738e2b9a5a7b658e631fce7046c2a32483aa9b25d8be9c631e5359af",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/vincenzoaellis/actions/runs/27163830209"
    }
  ]
}