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  "Title": "Yet Another TAxonomy Handler",
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  "Description": "Provides functions to manage taxonomy when lineages are\ndescribed with strings and ranks separated with special\npatterns like \"|*__\" or \";*__\".",
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  "_topics": [
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    "taxonomy"
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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      "date": "2019-06-28"
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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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      "name": "abundances",
      "title": "Abundance table for 199 samples.",
      "object": "abundances",
      "class": [
        "data.frame"
      ],
      "fields": [],
      "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": [
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      ]
    },
    {
      "page": "is_clade",
      "title": "Test if a lineage belongs to a clade",
      "topics": [
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      ]
    },
    {
      "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",
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        "is_rank"
      ]
    },
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      "page": "taxtable",
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      ]
    },
    {
      "page": "taxtree",
      "title": "Taxonomic tree",
      "topics": [
        "taxtree"
      ]
    },
    {
      "page": "trim_common",
      "title": "Trim lineages until the shallowest common rank.",
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        "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"
      ]
    }
  ],
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