{
  "_id": "6a10892dacfb0bcc41cb2860",
  "Package": "TRAMPR",
  "Title": "'TRFLP' Analysis and Matching Package for R",
  "Version": "1.0-11",
  "Authors@R": "c(person(\"Rich\", \"FitzJohn\", role = c(\"aut\", \"cre\"),\nemail = \"rich.fitzjohn@gmail.com\"),\nperson(\"Ian\", \"Dickie\", role = \"aut\"))",
  "License": "GPL-2",
  "URL": "https://github.com/richfitz/TRAMPR",
  "Description": "Matching terminal restriction fragment length polymorphism\n('TRFLP') profiles between unknown samples and a database of\nknown samples.  'TRAMPR' facilitates analysis of many unknown\nprofiles at once, and provides tools for working directly with\nelectrophoresis output through to generating summaries suitable\nfor community analyses with R's rich set of statistical\nfunctions.  'TRAMPR' also resolves the issues of multiple\n'TRFLP' profiles within a species, and shared 'TRFLP' profiles\nacross species.",
  "Repository": "https://richfitz.r-universe.dev",
  "Date/Publication": "2025-06-02 15:35:26 UTC",
  "RemoteUrl": "https://github.com/richfitz/trampr",
  "RemoteRef": "HEAD",
  "RemoteSha": "45682bd175c87c0c8d805061964ffc04035650b3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-05 07:27:29 UTC",
    "User": "root"
  },
  "Author": "Rich FitzJohn [aut, cre],\nIan Dickie [aut]",
  "Maintainer": "Rich FitzJohn <rich.fitzjohn@gmail.com>",
  "MD5sum": "8fca7b581d884cfe60bee15f03d48741",
  "_user": "richfitz",
  "_type": "src",
  "_file": "TRAMPR_1.0-11.tar.gz",
  "_fileid": "a39ee84265144180306661f2180212821fc276e900a1c8a38593ea73e3854a07",
  "_filesize": 505334,
  "_sha256": "a39ee84265144180306661f2180212821fc276e900a1c8a38593ea73e3854a07",
  "_created": "2026-05-05T07:27:29.000Z",
  "_published": "2026-05-22T16:49:49.602Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77424230530,
      "time": 104,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6800864319"
    },
    {
      "job": 77424230706,
      "time": 105,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6800866045"
    },
    {
      "job": 77424230550,
      "time": 89,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6800860635"
    },
    {
      "job": 77424230366,
      "time": 96,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6800862019"
    },
    {
      "job": 77424229816,
      "time": 167,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6800837314"
    },
    {
      "job": 77424229712,
      "time": 80,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7165848100"
    },
    {
      "job": 77424230140,
      "time": 71,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6800856152"
    },
    {
      "job": 77424230726,
      "time": 61,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6800853723"
    },
    {
      "job": 77424230410,
      "time": 70,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6800856759"
    }
  ],
  "_buildurl": "https://github.com/r-universe/richfitz/actions/runs/25363353880",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/richfitz/trampr",
  "_commit": {
    "id": "45682bd175c87c0c8d805061964ffc04035650b3",
    "author": "Rich FitzJohn <r.fitzjohn@imperial.ac.uk>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #3 from richfitz/update-authors\n\nUpdate authors ahead of CRAN change",
    "time": 1748878526
  },
  "_maintainer": {
    "name": "Rich FitzJohn",
    "email": "rich.fitzjohn@gmail.com",
    "login": "richfitz",
    "mastodon": "@richfitz@fosstodon.org",
    "uuid": 1558093
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.4",
      "role": "Depends"
    }
  ],
  "_owner": "richfitz",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-23",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "richfitz",
      "count": 28,
      "uuid": 1558093
    }
  ],
  "_userbio": {
    "uuid": 1558093,
    "type": "user",
    "name": "Rich FitzJohn"
  },
  "_downloads": {
    "count": 3072,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TRAMPR"
  },
  "_mentions": 4,
  "_devurl": "https://github.com/richfitz/trampr",
  "_searchresults": 23,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/TRAMPR.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/richfitz/trampr",
  "_realowner": "richfitz",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0-1",
      "date": "2006-11-13"
    },
    {
      "version": "1.0-2",
      "date": "2006-11-22"
    },
    {
      "version": "1.0-4",
      "date": "2007-06-05"
    },
    {
      "version": "1.0-5",
      "date": "2009-05-24"
    },
    {
      "version": "1.0-6",
      "date": "2009-10-15"
    },
    {
      "version": "1.0-7",
      "date": "2012-03-23"
    },
    {
      "version": "1.0-8",
      "date": "2016-06-09"
    },
    {
      "version": "1.0-9",
      "date": "2020-02-28"
    },
    {
      "version": "1.0-10",
      "date": "2022-02-07"
    }
  ],
  "_exports": [
    "[.TRAMPknowns",
    "[.TRAMPsamples",
    "absolute.min",
    "add.known",
    "add.known.TRAMP",
    "add.known.TRAMPknowns",
    "build.knowns",
    "classify",
    "combine",
    "combine.TRAMP",
    "combine.TRAMPknowns",
    "combine.TRAMPsamples",
    "create.diffsmatrix",
    "group.knowns",
    "group.knowns.TRAMP",
    "group.knowns.TRAMPknowns",
    "labels.TRAMPknowns",
    "labels.TRAMPsamples",
    "load.abi",
    "load.abi.create.info",
    "load.abi.create.template",
    "plot.TRAMP",
    "plot.TRAMPknowns",
    "read.abi",
    "read.TRAMPknowns",
    "read.TRAMPsamples",
    "rebuild.TRAMP",
    "remove.TRAMP.match",
    "summary.TRAMP",
    "summary.TRAMPknowns",
    "summary.TRAMPsamples",
    "TRAMP",
    "TRAMP.plotone",
    "TRAMPknowns",
    "TRAMPsamples",
    "TRAMPsamples.plotone",
    "update.TRAMP",
    "write.TRAMPknowns",
    "write.TRAMPsamples"
  ],
  "_datasets": [
    {
      "name": "demo.knowns",
      "title": "Demonstration Knowns Database",
      "object": "demo.knowns",
      "file": "demo.knowns.rda",
      "class": [
        "TRAMPknowns"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "demo.samples",
      "title": "Demonstration Samples Database",
      "object": "demo.samples",
      "file": "demo.samples.rda",
      "class": [
        "TRAMPsamples"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "TRAMPR-package",
      "title": "The TRAMPR Package (TRFLP Analysis and Matching Package for R)",
      "topics": [
        "TRAMPR-package",
        "TRAMPR"
      ]
    },
    {
      "page": "add.known",
      "title": "Add Knowns To TRAMPknowns Databases",
      "topics": [
        "add.known",
        "add.known.TRAMP",
        "add.known.TRAMPknowns",
        "combine.TRAMP",
        "combine.TRAMPknowns"
      ]
    },
    {
      "page": "build.knowns",
      "title": "Automatically Build Knowns Database",
      "topics": [
        "build.knowns"
      ]
    },
    {
      "page": "combine",
      "title": "Combine Two Objects",
      "topics": [
        "combine"
      ]
    },
    {
      "page": "combine.TRAMPsamples",
      "title": "Combine TRAMPsamples Objects",
      "topics": [
        "combine.TRAMPsamples"
      ]
    },
    {
      "page": "create.diffsmatrix",
      "title": "Calculate Matrix of Distances between Peaks",
      "topics": [
        "create.diffsmatrix"
      ]
    },
    {
      "page": "demo.knowns",
      "title": "Demonstration Knowns Database",
      "topics": [
        "demo.knowns"
      ]
    },
    {
      "page": "demo.samples",
      "title": "Demonstration Samples Database",
      "topics": [
        "demo.samples"
      ]
    },
    {
      "page": "group.knowns",
      "title": "Knowns Clustering",
      "topics": [
        "group.knowns",
        "group.knowns.TRAMP",
        "group.knowns.TRAMPknowns"
      ]
    },
    {
      "page": "load.abi",
      "title": "Load ABI Output Files",
      "topics": [
        "load.abi",
        "load.abi.create.info",
        "load.abi.create.template",
        "peakscanner.to.genemapper"
      ]
    },
    {
      "page": "plot.TRAMP",
      "title": "Plot a TRAMP Object",
      "topics": [
        "plot.TRAMP",
        "TRAMP.plotone"
      ]
    },
    {
      "page": "plot.TRAMPknowns",
      "title": "Summary Plot of Knowns Data",
      "topics": [
        "plot.TRAMPknowns"
      ]
    },
    {
      "page": "plot.TRAMPsamples",
      "title": "Plot a TRAMPsamples Object",
      "topics": [
        "plot.TRAMPsamples",
        "TRAMPsamples.plotone"
      ]
    },
    {
      "page": "read.abi",
      "title": "Read ABI Output Files",
      "topics": [
        "read.abi"
      ]
    },
    {
      "page": "read.write",
      "title": "Read/Write TRAMPknowns and TRAMPsamples Objects",
      "topics": [
        "read.TRAMPknowns",
        "read.TRAMPsamples",
        "write.TRAMPknowns",
        "write.TRAMPsamples"
      ]
    },
    {
      "page": "rebuild.TRAMP",
      "title": "Rebuild a TRAMP Object",
      "topics": [
        "rebuild.TRAMP"
      ]
    },
    {
      "page": "remove.TRAMP.match",
      "title": "Mark a TRAMP Match as Ignored",
      "topics": [
        "remove.TRAMP.match"
      ]
    },
    {
      "page": "summary.TRAMP",
      "title": "Create Presence/Absence Matrices from TRAMP Objects",
      "topics": [
        "summary.TRAMP"
      ]
    },
    {
      "page": "TRAMP",
      "title": "TRFLP Analysis and Matching Program",
      "topics": [
        "TRAMP"
      ]
    },
    {
      "page": "TRAMPindexing",
      "title": "Index (Subset) TRAMPsamples and TRAMPknowns Objects",
      "topics": [
        "TRAMPindexing",
        "[.TRAMPknowns",
        "[.TRAMPsamples"
      ]
    },
    {
      "page": "TRAMPknowns",
      "title": "TRAMPknowns Objects",
      "topics": [
        "labels.TRAMPknowns",
        "summary.TRAMPknowns",
        "TRAMPknowns"
      ]
    },
    {
      "page": "TRAMPsamples",
      "title": "TRAMPsamples Objects",
      "topics": [
        "labels.TRAMPsamples",
        "summary.TRAMPsamples",
        "TRAMPsamples"
      ]
    },
    {
      "page": "update.TRAMP",
      "title": "Interactively Alter a TRAMP Object",
      "topics": [
        "update.TRAMP"
      ]
    }
  ],
  "_readme": "https://github.com/richfitz/trampr/raw/HEAD/README.md",
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "TRAMPRdemo.Rnw",
      "filename": "TRAMPRdemo.pdf",
      "title": "Introduction to TRAMPR",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2012-03-23 17:54:02",
      "modified": "2022-02-07 18:48:13",
      "commits": 3
    }
  ],
  "_score": 5.150179043041049,
  "_indexed": true,
  "_nocasepkg": "trampr",
  "_universes": [
    "richfitz"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0-11",
      "date": "2026-05-05T07:29:14.000Z",
      "distro": "noble",
      "commit": "45682bd175c87c0c8d805061964ffc04035650b3",
      "fileid": "a0b4cdd3472983bfa91422d02c68c21728aa53aa3350f87680929db1fce3b9ee",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/richfitz/actions/runs/25363353880"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0-11",
      "date": "2026-05-05T07:29:21.000Z",
      "distro": "noble",
      "commit": "45682bd175c87c0c8d805061964ffc04035650b3",
      "fileid": "87974a1e23daf108978ea99a2144e9c5de3b79af6116692d48c8677ea4be6f89",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/richfitz/actions/runs/25363353880"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0-11",
      "date": "2026-05-05T07:29:04.000Z",
      "commit": "45682bd175c87c0c8d805061964ffc04035650b3",
      "fileid": "c5c95819cd1623d3cb31e9aa88224e6abab55f8b17fbfb3ed7fb704a8c694562",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/richfitz/actions/runs/25363353880"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0-11",
      "date": "2026-05-05T07:29:04.000Z",
      "commit": "45682bd175c87c0c8d805061964ffc04035650b3",
      "fileid": "d727e882cc225b97694a7b8859259e3a6314004479ce1786ae1945a354863a58",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/richfitz/actions/runs/25363353880"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0-11",
      "date": "2026-05-05T07:28:36.000Z",
      "commit": "45682bd175c87c0c8d805061964ffc04035650b3",
      "fileid": "cc7e262f1a01625a92c001cd8fa868a40b07f388cc6beda2d0754c433af0dd47",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/richfitz/actions/runs/25363353880"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0-11",
      "date": "2026-05-05T07:28:29.000Z",
      "commit": "45682bd175c87c0c8d805061964ffc04035650b3",
      "fileid": "9f04e5efcc70f4887c6c51f3d2b60a20db1a1ddf6908cbbaa5098c6676f0b224",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/richfitz/actions/runs/25363353880"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0-11",
      "date": "2026-05-05T07:28:41.000Z",
      "commit": "45682bd175c87c0c8d805061964ffc04035650b3",
      "fileid": "88630fc5a054977eafbd523670f20aaad11791fc00041badc92a34af2624bdd3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/richfitz/actions/runs/25363353880"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0-11",
      "date": "2026-05-22T16:49:36.000Z",
      "commit": "45682bd175c87c0c8d805061964ffc04035650b3",
      "fileid": "397b4c7aff2a7505357eeeedd23dd51d291073eb4667df2d06168efe60d84f74",
      "status": "success",
      "buildurl": "https://github.com/r-universe/richfitz/actions/runs/25363353880"
    }
  ]
}