{
  "_id": "6a129d9dacfb0bcc41d0f820",
  "Package": "taxonomizr",
  "Maintainer": "Scott Sherrill-Mix <ssm@msu.edu>",
  "License": "GPL (>=2) | file LICENSE",
  "Title": "Functions to Work with NCBI Accessions and Taxonomy",
  "Type": "Package",
  "LazyLoad": "yes",
  "Author": "Scott Sherrill-Mix [aut, cre]",
  "Authors@R": "c(person(\"Scott\", \"Sherrill-Mix\", role = c(\"aut\", \"cre\"),\nemail = \"ssm@msu.edu\"))",
  "BugReports": "https://github.com/sherrillmix/taxonomizr/issues",
  "Description": "Functions for assigning taxonomy to NCBI accession numbers\nand taxon IDs based on NCBI's accession2taxid and taxdump\nfiles. This package allows the user to download NCBI data dumps\nand create a local database for fast and local taxonomic\nassignment.",
  "URL": "https://github.com/sherrillmix/taxonomizr/",
  "Version": "0.11.2",
  "Date": "2025-07-23",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "libssl-dev",
  "Repository": "https://sherrillmix.r-universe.dev",
  "Date/Publication": "2025-07-24 03:15:19 UTC",
  "RemoteUrl": "https://github.com/sherrillmix/taxonomizr",
  "RemoteRef": "HEAD",
  "RemoteSha": "218641b806f4aa31ad88f0d0b5c403cf4de5704b",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-22 09:22:53 UTC",
    "User": "root"
  },
  "MD5sum": "106f577d39211882879f9a2d8b0efc1a",
  "_user": "sherrillmix",
  "_type": "src",
  "_file": "taxonomizr_0.11.2.tar.gz",
  "_fileid": "0fd849faee26b29d4f6bf528726788b8347987b800e925636875f9ca99c8bd9f",
  "_filesize": 269892,
  "_sha256": "0fd849faee26b29d4f6bf528726788b8347987b800e925636875f9ca99c8bd9f",
  "_created": "2026-05-22T09:22:53.000Z",
  "_published": "2026-05-24T06:41:33.032Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77574773224,
      "time": 3722,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 77574773310,
      "time": 143,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7157217703"
    },
    {
      "job": 77574773230,
      "time": 3716,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 77574773281,
      "time": 151,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7157219866"
    },
    {
      "job": 77574773359,
      "time": 149,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7157211843"
    },
    {
      "job": 77574773360,
      "time": 260,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7157247313"
    },
    {
      "job": 77574773328,
      "time": 247,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7157235677"
    },
    {
      "job": 77574773347,
      "time": 298,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7157258644"
    },
    {
      "job": 77574773335,
      "time": 169,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7157171270"
    },
    {
      "job": 77574773327,
      "time": 104,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7157205473"
    },
    {
      "job": 77574773376,
      "time": 139,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7157216932"
    },
    {
      "job": 77574773331,
      "time": 100,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7157203815"
    },
    {
      "job": 77574773286,
      "time": 138,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7157215456"
    }
  ],
  "_buildurl": "https://github.com/r-universe/sherrillmix/actions/runs/26279460698",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/sherrillmix/taxonomizr",
  "_commit": {
    "id": "218641b806f4aa31ad88f0d0b5c403cf4de5704b",
    "author": "sherrillmix <sherrillmix@users.noreply.github.com>",
    "committer": "sherrillmix <sherrillmix@users.noreply.github.com>",
    "message": "Rerender docs\n",
    "time": 1753326919
  },
  "_maintainer": {
    "name": "Scott Sherrill-Mix",
    "email": "ssm@msu.edu"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "RSQLite",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "curl",
      "version": ">= 5.0.0",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "sherrillmix",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-30",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 81,
  "_contributors": [
    {
      "user": "sherrillmix",
      "count": 311,
      "uuid": 1217152
    }
  ],
  "_userbio": {
    "uuid": 1217152,
    "type": "user",
    "name": "Scott Sherrill-Mix"
  },
  "_downloads": {
    "count": 461,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/taxonomizr"
  },
  "_mentions": 4,
  "_devurl": "https://github.com/sherrillmix/taxonomizr",
  "_searchresults": 303,
  "_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/taxonomizr.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/sherrillmix/taxonomizr",
  "_realowner": "sherrillmix",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.2.2",
      "date": "2017-03-09"
    },
    {
      "version": "0.5.1",
      "date": "2018-08-31"
    },
    {
      "version": "0.5.3",
      "date": "2019-04-22"
    },
    {
      "version": "0.6.0",
      "date": "2021-02-09"
    },
    {
      "version": "0.7.1",
      "date": "2021-04-23"
    },
    {
      "version": "0.8.0",
      "date": "2021-05-07"
    },
    {
      "version": "0.9.2",
      "date": "2022-06-23"
    },
    {
      "version": "0.9.3",
      "date": "2022-06-26"
    },
    {
      "version": "0.10.2",
      "date": "2023-01-31"
    },
    {
      "version": "0.10.6",
      "date": "2023-12-16"
    },
    {
      "version": "0.10.7",
      "date": "2025-01-08"
    },
    {
      "version": "0.10.8",
      "date": "2025-02-27"
    },
    {
      "version": "0.11.1",
      "date": "2025-03-13"
    }
  ],
  "_exports": [
    "accessionToTaxa",
    "condenseTaxa",
    "getAccession2taxid",
    "getAccessions",
    "getCommon",
    "getDescendants",
    "getId",
    "getId2",
    "getNamesAndNodes",
    "getRawTaxonomy",
    "getTaxonomy",
    "getTaxonomy2",
    "lastNotNa",
    "makeNewick",
    "normalizeTaxa",
    "prepareDatabase",
    "read.accession2taxid",
    "read.names",
    "read.names.sql",
    "read.nodes",
    "read.nodes.sql",
    "streamingRead",
    "topoSort"
  ],
  "_help": [
    {
      "page": "accessionToTaxa",
      "title": "Convert accessions to taxa",
      "topics": [
        "accessionToTaxa"
      ]
    },
    {
      "page": "condenseTaxa",
      "title": "Condense multiple taxonomic assignments to their most recent common branch",
      "topics": [
        "condenseTaxa"
      ]
    },
    {
      "page": "getAccession2taxid",
      "title": "Download accession2taxid files from NCBI",
      "topics": [
        "getAccession2taxid"
      ]
    },
    {
      "page": "getAccessions",
      "title": "Find all accessions for a taxa",
      "topics": [
        "getAccessions"
      ]
    },
    {
      "page": "getCommon",
      "title": "Find common names for a given taxa",
      "topics": [
        "getCommon"
      ]
    },
    {
      "page": "getDescendants",
      "title": "Get descendant ranks for a taxa",
      "topics": [
        "getDescendants"
      ]
    },
    {
      "page": "getId",
      "title": "Find a given taxa by name",
      "topics": [
        "getId"
      ]
    },
    {
      "page": "getId2",
      "title": "Find a given taxa by name",
      "topics": [
        "getId2"
      ]
    },
    {
      "page": "getNamesAndNodes",
      "title": "Download names and nodes files from NCBI",
      "topics": [
        "getNamesAndNodes"
      ]
    },
    {
      "page": "getRawTaxonomy",
      "title": "Get all taxonomy for a taxa",
      "topics": [
        "getRawTaxonomy"
      ]
    },
    {
      "page": "getTaxonomy",
      "title": "Get taxonomic ranks for a taxa",
      "topics": [
        "getTaxonomy"
      ]
    },
    {
      "page": "getTaxonomy2",
      "title": "Get taxonomic ranks for a taxa",
      "topics": [
        "getTaxonomy2"
      ]
    },
    {
      "page": "lastNotNa",
      "title": "Return last not NA value",
      "topics": [
        "lastNotNa"
      ]
    },
    {
      "page": "makeNewick",
      "title": "Create a Newick tree from taxonomy",
      "topics": [
        "makeNewick"
      ]
    },
    {
      "page": "normalizeTaxa",
      "title": "Bring multiple raw taxonomies into alignment",
      "topics": [
        "normalizeTaxa"
      ]
    },
    {
      "page": "prepareDatabase",
      "title": "Download data from NCBI and set up SQLite database",
      "topics": [
        "prepareDatabase"
      ]
    },
    {
      "page": "read.accession2taxid",
      "title": "Read NCBI accession2taxid files",
      "topics": [
        "read.accession2taxid"
      ]
    },
    {
      "page": "read.names",
      "title": "Read NCBI names file",
      "topics": [
        "read.names"
      ]
    },
    {
      "page": "read.names.sql",
      "title": "Read NCBI names file",
      "topics": [
        "read.names.sql"
      ]
    },
    {
      "page": "read.nodes",
      "title": "Read NCBI nodes file",
      "topics": [
        "read.nodes"
      ]
    },
    {
      "page": "read.nodes.sql",
      "title": "Read NCBI nodes file",
      "topics": [
        "read.nodes.sql"
      ]
    },
    {
      "page": "resumableDownload",
      "title": "Download file using curl allowing resumption of interrupted files",
      "topics": [
        "resumableDownload"
      ]
    },
    {
      "page": "streamingRead",
      "title": "Process a large file piecewise",
      "topics": [
        "streamingRead"
      ]
    },
    {
      "page": "taxonomizrSwitch",
      "title": "Switch from data.table to SQLite",
      "topics": [
        "taxonomizrSwitch"
      ]
    },
    {
      "page": "topoSort",
      "title": "Combine multiple sorted vectors into a single sorted vector",
      "topics": [
        "topoSort"
      ]
    },
    {
      "page": "trimTaxa",
      "title": "Trim columns from taxa file",
      "topics": [
        "trimTaxa"
      ]
    }
  ],
  "_readme": "https://github.com/sherrillmix/taxonomizr/raw/HEAD/README.md",
  "_rundeps": [
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "curl",
    "data.table",
    "DBI",
    "fastmap",
    "glue",
    "lifecycle",
    "memoise",
    "pkgconfig",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "rlang",
    "RSQLite",
    "vctrs"
  ],
  "_vignettes": [
    {
      "source": "usage.Rmd",
      "filename": "usage.html",
      "title": "taxonomizr usage",
      "author": "Scott Sherrill-Mix",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Requirements",
        "Installation",
        "Preparation<a name=\"preparation\"></a>",
        "Assigning taxonomy",
        "Producing accession numbers",
        "Finding taxonomy for NCBI accession numbers",
        "Finding taxonomy for taxonomic names",
        "Finding descendants for a given taxa",
        "Finding common names for taxonomic IDs",
        "Condensing taxonomy a.k.a. lowest common ancestor LCA",
        "Find all taxonomic assignments for a given taxa",
        "Finding accessions for a given taxonomic ID",
        "Convert taxonomy to Newick tree",
        "Note: NCBI name changes in early 2023",
        "Changelog",
        "v0.11.1",
        "v0.10.8",
        "v0.10.7",
        "v0.10.6",
        "v0.10.5",
        "v0.10.4",
        "v0.10.3",
        "v0.10.2",
        "v0.10.1",
        "v0.9.4",
        "v0.9.3",
        "v0.9.2",
        "v0.8.4",
        "v0.8.3",
        "v0.8.2",
        "v0.8.1",
        "v0.8.0",
        "v0.7.1",
        "v0.7.0",
        "v0.6.0",
        "v0.5.3",
        "v0.5.0",
        "Manual preparation of database (usually not necessary)",
        "Download names and nodes",
        "Download accession to taxa files",
        "Convert names, nodes and accessions to database",
        "Switch from data.table to SQLite"
      ],
      "created": "2017-03-07 19:00:36",
      "modified": "2025-03-12 21:07:47",
      "commits": 52
    }
  ],
  "_score": 8.168078897764598,
  "_indexed": true,
  "_nocasepkg": "taxonomizr",
  "_universes": [
    "sherrillmix"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.11.2",
      "date": "2026-05-22T09:24:56.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "218641b806f4aa31ad88f0d0b5c403cf4de5704b",
      "fileid": "8d55384b755cccab41f2332d0900727ea4e3ba5f6fc1774aaa9d3fdb4eceb9b5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sherrillmix/actions/runs/26279460698"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.11.2",
      "date": "2026-05-22T09:25:02.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "218641b806f4aa31ad88f0d0b5c403cf4de5704b",
      "fileid": "b0c2afea60c4bc13a66082f0f680ccd5c34389f380afb7254de9a6313dad5241",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sherrillmix/actions/runs/26279460698"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.11.2",
      "date": "2026-05-22T09:24:52.000Z",
      "arch": "aarch64",
      "commit": "218641b806f4aa31ad88f0d0b5c403cf4de5704b",
      "fileid": "ba77a5cca999dc47129ee95b3835cf6e2a04ea95a65942d953f1637c51e73be2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sherrillmix/actions/runs/26279460698"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.11.2",
      "date": "2026-05-22T09:26:16.000Z",
      "arch": "x86_64",
      "commit": "218641b806f4aa31ad88f0d0b5c403cf4de5704b",
      "fileid": "e742b2e04e7ca9035b07f572fb1d210485117cbc730414163d7c29b7a1feb772",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sherrillmix/actions/runs/26279460698"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.11.2",
      "date": "2026-05-22T09:25:34.000Z",
      "arch": "aarch64",
      "commit": "218641b806f4aa31ad88f0d0b5c403cf4de5704b",
      "fileid": "445c84e835835815c8859fcde6923fb87d2b0f7d9fb81a94d1e727ebc848793c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sherrillmix/actions/runs/26279460698"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.11.2",
      "date": "2026-05-22T09:26:30.000Z",
      "arch": "x86_64",
      "commit": "218641b806f4aa31ad88f0d0b5c403cf4de5704b",
      "fileid": "bca400c5cd4c6972b072cf2164fd76c971066099fd8742d950fa15e40b42f23c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sherrillmix/actions/runs/26279460698"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.11.2",
      "date": "2026-05-22T09:24:52.000Z",
      "arch": "emscripten",
      "commit": "218641b806f4aa31ad88f0d0b5c403cf4de5704b",
      "fileid": "e28ea35f68a65916883c2462b3540e4c5ebc9c8354ba9cf90e1b712608f368b0",
      "status": "success",
      "buildurl": "https://github.com/r-universe/sherrillmix/actions/runs/26279460698"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.11.2",
      "date": "2026-05-22T09:24:27.000Z",
      "arch": "x86_64",
      "commit": "218641b806f4aa31ad88f0d0b5c403cf4de5704b",
      "fileid": "fa7558b6c5de2014df361290bf1c4afdd44e5a360bc8c3c7cc5dc4827cb992f9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sherrillmix/actions/runs/26279460698"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.11.2",
      "date": "2026-05-22T09:23:52.000Z",
      "arch": "x86_64",
      "commit": "218641b806f4aa31ad88f0d0b5c403cf4de5704b",
      "fileid": "bbab59dd1f778fef986a5e561f5fa75e62c2fad542ae3aa1e9134b6a34a6b54a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sherrillmix/actions/runs/26279460698"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.11.2",
      "date": "2026-05-22T09:24:02.000Z",
      "arch": "x86_64",
      "commit": "218641b806f4aa31ad88f0d0b5c403cf4de5704b",
      "fileid": "448487280411651d0150e069f2546562587b7b1bf46c0c1b93375965979e97bd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sherrillmix/actions/runs/26279460698"
    }
  ]
}