{
  "_id": "6ad322112c5c76d3dd0c99ea",
  "Package": "vhica",
  "Type": "Package",
  "Title": "Vertical and Horizontal Inheritance Consistence Analysis",
  "Version": "0.2.9",
  "Date": "2025-08-13",
  "Authors@R": "person(given = \"Arnaud\",\nfamily = \"Le Rouzic\",\nrole = c(\"aut\", \"cre\"),\nemail = \"arnaud.le-rouzic@universite-paris-saclay.fr\")",
  "Maintainer": "Arnaud Le Rouzic\n<arnaud.le-rouzic@universite-paris-saclay.fr>",
  "Description": "The \"Vertical and Horizontal Inheritance Consistence\nAnalysis\" method is described in the following publication:\n\"VHICA: a new method to discriminate between vertical and\nhorizontal transposon transfer: application to the mariner\nfamily within Drosophila\" by G. Wallau. et al. (2016)\n<DOI:10.1093/molbev/msv341>. The purpose of the method is to\ndetect horizontal transfers of transposable elements, by\ncontrasting the divergence of transposable element sequences\nwith that of regular genes.",
  "License": "GPL-2",
  "Repository": "https://lerouzic.r-universe.dev",
  "Date/Publication": "2025-08-23 13:28:19 UTC",
  "RemoteUrl": "https://github.com/lerouzic/vhica",
  "RemoteRef": "HEAD",
  "RemoteSha": "b234380a8931b82666f7c20d977c62e64b25dbc5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-17 07:14:33 UTC",
    "User": "root"
  },
  "Author": "Arnaud Le Rouzic [aut, cre]",
  "_user": "lerouzic",
  "_type": "src",
  "_file": "vhica_0.2.9.tar.gz",
  "_fileid": "https://r2.ropensci.org/91963b51e8c679a2460073c99fb094a5075e960411e9f42cd43344480d786589",
  "_filesize": 151701,
  "_sha256": "91963b51e8c679a2460073c99fb094a5075e960411e9f42cd43344480d786589",
  "_expires": "2027-01-25T07:21:51.000Z",
  "_created": "2026-10-17T07:14:33.000Z",
  "_published": "2026-10-17T07:21:53.201Z",
  "_buildurl": "https://github.com/r-universe/lerouzic/actions/runs/39012767265",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 117339046828,
      "time": 99,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12093478050"
    },
    {
      "job": 117339046825,
      "time": 88,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12092674686"
    },
    {
      "job": 117339046829,
      "time": 201,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12093926199"
    },
    {
      "job": 117339046827,
      "time": 202,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12093636904"
    },
    {
      "job": 117338651575,
      "time": 127,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12092629707"
    },
    {
      "job": 117339046801,
      "time": 74,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12092629809"
    },
    {
      "job": 117339046872,
      "time": 62,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "12094020588"
    },
    {
      "job": 117339046853,
      "time": 88,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "12094205252"
    },
    {
      "job": 117339046857,
      "time": 67,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12093687019"
    }
  ],
  "_upstream": "https://github.com/lerouzic/vhica",
  "_commit": {
    "id": "b234380a8931b82666f7c20d977c62e64b25dbc5",
    "author": "Arnaud Le Rouzic <lerouzic@egce.cnrs-gif.fr>",
    "committer": "Arnaud Le Rouzic <lerouzic@egce.cnrs-gif.fr>",
    "message": "Oops, removing one note for CRAN submission.\n",
    "time": 1755955699
  },
  "_maintainer": {
    "name": "Arnaud Le Rouzic",
    "email": "arnaud.le-rouzic@universite-paris-saclay.fr",
    "login": "lerouzic",
    "twitter": "@ArnaudLeRouzic",
    "description": "",
    "uuid": 58432423
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "ape",
      "role": "Suggests"
    },
    {
      "package": "plotrix",
      "role": "Suggests"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    },
    {
      "package": "seqinr",
      "role": "Suggests"
    },
    {
      "package": "gtools",
      "role": "Suggests"
    }
  ],
  "_owner": "lerouzic",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "lerouzic",
      "count": 4,
      "uuid": 58432423
    }
  ],
  "_userbio": {
    "uuid": 58432423,
    "type": "user",
    "name": "Arnaud Le Rouzic",
    "followers": 5
  },
  "_downloads": {
    "count": 359,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/vhica"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/lerouzic/vhica",
  "_searchresults": 6,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md",
    "extra/vhica.html"
  ],
  "_homeurl": "https://github.com/lerouzic/vhica",
  "_realowner": "lerouzic",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.2.4",
      "date": "2016-04-05"
    },
    {
      "version": "0.2.7",
      "date": "2020-03-02"
    },
    {
      "version": "0.2.8",
      "date": "2023-03-08"
    },
    {
      "version": "0.2.9",
      "date": "2025-08-23"
    }
  ],
  "_exports": [
    "CUB",
    "div",
    "read.vhica"
  ],
  "_help": [
    {
      "page": "vhica-package",
      "title": "Vertical and Horizontal Inheritance Consistence Analysis",
      "topics": [
        "vhica-package",
        "vhica"
      ]
    },
    {
      "page": "CUB",
      "title": "Computes the Codon Usage Bias of DNA sequences",
      "topics": [
        "CUB"
      ]
    },
    {
      "page": "div",
      "title": "Computation of the synonymous divergence between sequences",
      "topics": [
        "div"
      ]
    },
    {
      "page": "image.vhica",
      "title": "Consistency matrix for a transposable element in the VHICA analysis.",
      "topics": [
        "image.vhica"
      ]
    },
    {
      "page": "plot.vhica",
      "title": "Plots a VHICA regression between two species.",
      "topics": [
        "plot.vhica"
      ]
    },
    {
      "page": "read.vhica",
      "title": "Reads divergence and codon usage data files for the VHICA method.",
      "topics": [
        "read.vhica"
      ]
    },
    {
      "page": "summary.vhicaimage",
      "title": "Provides a data.frame that nicely displays the information returned by 'image.vhica'.",
      "topics": [
        "summary.vhicaimage"
      ]
    }
  ],
  "_readme": "https://github.com/lerouzic/vhica/raw/HEAD/README.md",
  "_rundeps": [],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "vhica",
  "_universes": [
    "lerouzic"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.9",
      "date": "2026-10-17T07:16:16.000Z",
      "distro": "resolute",
      "commit": "b234380a8931b82666f7c20d977c62e64b25dbc5",
      "fileid": "https://r2.ropensci.org/05899b7d063ac839da8e0fa2993b8905fa76af2e5a73415967c2f17bc46f767f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lerouzic/actions/runs/39012767265"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.2.9",
      "date": "2026-10-17T07:16:05.000Z",
      "distro": "resolute",
      "commit": "b234380a8931b82666f7c20d977c62e64b25dbc5",
      "fileid": "https://r2.ropensci.org/a85ee5f3ed04653849d30fd16c4dbd5ccb691a29ee53f6163096c98124658d8f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lerouzic/actions/runs/39012767265"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.9",
      "date": "2026-10-17T07:19:49.000Z",
      "commit": "b234380a8931b82666f7c20d977c62e64b25dbc5",
      "fileid": "https://r2.ropensci.org/3a716aa47acf547f8e37f786be4ac18ec516edee130503d46c23d1c2a53ff453",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lerouzic/actions/runs/39012767265"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.2.9",
      "date": "2026-10-17T07:20:28.000Z",
      "commit": "b234380a8931b82666f7c20d977c62e64b25dbc5",
      "fileid": "https://r2.ropensci.org/ee012a72816034184e61ea8762c4f07e6b2bc3ed4803dab4b40f59e97684d04c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lerouzic/actions/runs/39012767265"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.2.9",
      "date": "2026-10-17T07:16:03.000Z",
      "commit": "b234380a8931b82666f7c20d977c62e64b25dbc5",
      "fileid": "https://r2.ropensci.org/9ab86b4851d91004da6b69247bd82b77a8b7820adb10a60d5eb70ea9a7c83f60",
      "status": "success",
      "buildurl": "https://github.com/r-universe/lerouzic/actions/runs/39012767265"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.9",
      "date": "2026-10-17T07:15:34.000Z",
      "commit": "b234380a8931b82666f7c20d977c62e64b25dbc5",
      "fileid": "https://r2.ropensci.org/6e27765730232a6f1855bead2dd1173c0aebbd1b5b4da345439a43082785362c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lerouzic/actions/runs/39012767265"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.2.9",
      "date": "2026-10-17T07:15:59.000Z",
      "commit": "b234380a8931b82666f7c20d977c62e64b25dbc5",
      "fileid": "https://r2.ropensci.org/5947c7ca1c6753e0e2641216cc7147868a4e606c435de274d6daa37f1b5d527c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lerouzic/actions/runs/39012767265"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.2.9",
      "date": "2026-10-17T07:15:42.000Z",
      "commit": "b234380a8931b82666f7c20d977c62e64b25dbc5",
      "fileid": "https://r2.ropensci.org/c27316f4e9e37a924bd654c6e9761864bba72ae43cb1a08349905f58f5be77fd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/lerouzic/actions/runs/39012767265"
    }
  ]
}