{
  "_id": "6a1f0735b401979e7341be1b",
  "Package": "yatah",
  "Title": "Yet Another TAxonomy Handler",
  "Version": "1.0.0",
  "Authors@R": "person(\"Antoine\", \"Bichat\", , \"antoine.bichat@proton.me\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-6599-7081\"))",
  "Description": "Provides functions to manage taxonomy when lineages are\ndescribed with strings and ranks separated with special\npatterns like \"|*__\" or \";*__\".",
  "License": "GPL-3",
  "URL": "https://abichat.github.io/yatah/,\nhttps://github.com/abichat/yatah/",
  "BugReports": "https://github.com/abichat/yatah/issues",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.1",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://abichat.r-universe.dev",
  "Date/Publication": "2024-04-13 15:06:24 UTC",
  "RemoteUrl": "https://github.com/abichat/yatah",
  "RemoteRef": "HEAD",
  "RemoteSha": "d5476361fb39818eeeb2129c2d180101e266372b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-18 06:53:01 UTC",
    "User": "root"
  },
  "Author": "Antoine Bichat [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-6599-7081>)",
  "Maintainer": "Antoine Bichat <antoine.bichat@proton.me>",
  "MD5sum": "351dc4b79b739dcf5d3f9b3996506c2c",
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  "_type": "src",
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  "_created": "2026-05-18T06:53:01.000Z",
  "_published": "2026-06-02T16:39:17.554Z",
  "_distro": "noble",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/abichat/actions/runs/26018129019",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/abichat/yatah",
  "_commit": {
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    "author": "Antoine Bichat <30300749+abichat@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #17 from abichat/dev\n\nv1.0.0",
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  "_maintainer": {
    "name": "Antoine Bichat",
    "email": "antoine.bichat@proton.me",
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  },
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  "_dependencies": [
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    },
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      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "lifecycle",
      "role": "Imports"
    },
    {
      "package": "purrr",
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    },
    {
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    },
    {
      "package": "stringr",
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    },
    {
      "package": "dplyr",
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    },
    {
      "package": "knitr",
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    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
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    },
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  "_owner": "abichat",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "clades",
    "taxonomy"
  ],
  "_stars": 6,
  "_contributors": [
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      "count": 147,
      "uuid": 30300749
    },
    {
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      "uuid": 21193866
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  "_userbio": {
    "uuid": 30300749,
    "type": "user",
    "name": "Antoine Bichat",
    "description": "Computational Scientist\r\n#RStats #DataScience"
  },
  "_downloads": {
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/yatah"
  },
  "_devurl": "https://github.com/abichat/yatah",
  "_pkgdown": "https://abichat.github.io/yatah/",
  "_searchresults": 15,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/yatah.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/abichat/yatah",
  "_realowner": "abichat",
  "_cranurl": true,
  "_releases": [
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      "version": "0.0.1",
      "date": "2019-06-28"
    },
    {
      "version": "0.1.0",
      "date": "2020-03-01"
    },
    {
      "version": "0.2.1",
      "date": "2022-11-13"
    },
    {
      "version": "1.0.0",
      "date": "2024-04-13"
    }
  ],
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    "get_all_clades",
    "get_clade",
    "get_last_clade",
    "get_last_rank",
    "is_at_least_rank",
    "is_clade",
    "is_lineage",
    "is_rank",
    "last_clade",
    "last_rank",
    "taxtable",
    "taxtree",
    "trim_common",
    "trim_rank",
    "trim_void"
  ],
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      "rows": 1585,
      "table": true,
      "tojson": true
    },
    {
      "name": "all_ranks",
      "title": "Ranks handled by 'yatah'",
      "object": "all_ranks",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "abundances",
      "title": "Abundance table for 199 samples.",
      "topics": [
        "abundances"
      ]
    },
    {
      "page": "all_ranks",
      "title": "Ranks handled by 'yatah'",
      "topics": [
        "all_ranks"
      ]
    },
    {
      "page": "get_all_clades",
      "title": "Extract all clades present in the lineages",
      "topics": [
        "get_all_clades"
      ]
    },
    {
      "page": "get_clade",
      "title": "Extract the clade of a desired rank in a lineage",
      "topics": [
        "get_clade"
      ]
    },
    {
      "page": "get_last_clade",
      "title": "Extract the last clade of a lineage",
      "topics": [
        "get_last_clade"
      ]
    },
    {
      "page": "get_last_rank",
      "title": "Extract the last rank of a lineage",
      "topics": [
        "get_last_rank"
      ]
    },
    {
      "page": "is_clade",
      "title": "Test if a lineage belongs to a clade",
      "topics": [
        "is_clade"
      ]
    },
    {
      "page": "is_lineage",
      "title": "Test if a string is a lineage",
      "topics": [
        "is_lineage"
      ]
    },
    {
      "page": "is_rank",
      "title": "Test if a lineage goes down to a specified rank",
      "topics": [
        "is_at_least_rank",
        "is_rank"
      ]
    },
    {
      "page": "taxtable",
      "title": "Taxonomic table",
      "topics": [
        "taxtable"
      ]
    },
    {
      "page": "taxtree",
      "title": "Taxonomic tree",
      "topics": [
        "taxtree"
      ]
    },
    {
      "page": "trim_common",
      "title": "Trim lineages until the shallowest common rank.",
      "topics": [
        "trim_common"
      ]
    },
    {
      "page": "trim_rank",
      "title": "Trim lineages until a specified rank",
      "topics": [
        "trim_rank"
      ]
    },
    {
      "page": "trim_void",
      "title": "Trim void ranks in lineages",
      "topics": [
        "trim_void"
      ]
    }
  ],
  "_pkglogo": "https://github.com/abichat/yatah/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/abichat/yatah/raw/HEAD/README.md",
  "_rundeps": [
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    "lattice",
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      "source": "gammaproteobacteria.Rmd",
      "filename": "gammaproteobacteria.html",
      "title": "Taxonomy of Gammaproteobacteria",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Data",
        "Filtering",
        "Taxonomic table",
        "Taxonomic tree",
        "References"
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      "created": "2019-04-06 14:44:21",
      "modified": "2024-04-13 15:06:24",
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