{
  "_id": "6a48b839e06c18f0a65487d6",
  "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",
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    "Date": "2026-07-04 06:54:54 UTC",
    "User": "root"
  },
  "Author": "Rich FitzJohn [aut, cre],\nIan Dickie [aut]",
  "Maintainer": "Rich FitzJohn <rich.fitzjohn@gmail.com>",
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  "_file": "TRAMPR_1.0-11.tar.gz",
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  "_created": "2026-07-04T06:54:54.000Z",
  "_published": "2026-07-04T07:37:29.025Z",
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    "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",
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    "email": "rich.fitzjohn@gmail.com",
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    "description": "",
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  "_rbuild": "4.6.1",
  "_assets": [
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    "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": [
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      "version": "1.0-1",
      "date": "2006-11-13"
    },
    {
      "version": "1.0-2",
      "date": "2006-11-22"
    },
    {
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      "date": "2007-06-05"
    },
    {
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      "date": "2009-05-24"
    },
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    },
    {
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      "date": "2012-03-23"
    },
    {
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      "date": "2016-06-09"
    },
    {
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      "date": "2020-02-28"
    },
    {
      "version": "1.0-10",
      "date": "2022-02-07"
    }
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  "_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",
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      "source": "TRAMPRdemo.Rnw",
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      "created": "2012-03-23 17:54:02",
      "modified": "2022-02-07 18:48:13",
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  "_indexed": true,
  "_nocasepkg": "trampr",
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