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  "Title": "Prioritize and Delete Erroneous Taxa in a Large Phylogenetic\nTree",
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  "Authors@R": "c(person(given=\"Satoshi\",family=\"Aoki\",role=c(\"aut\",\"cph\",\"cre\"),email=\"aokis1ll1@gmail.com\"),person(given=\"Keita\",family=\"Fukasawa\",role=\"ctb\"))",
  "Date": "2024-07-10",
  "Description": "Finds, prioritizes and deletes erroneous taxa in a\nphylogenetic tree. This package calculates scores for taxa in a\ntree. Higher score means the taxon is more erroneous. If the\nscore is zero for a taxon, the taxon is not erroneous. This\npackage also can remove all erroneous taxa automatically by\niterating score calculation and pruning taxa with the highest\nscore.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
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  "BugReports": "https://github.com/Sa-to-shi-A-o-ki/Apoderoides/issues",
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    "calcIntScore_C",
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    "getRankCentroid_C",
    "getRankMRCA",
    "getTipNo_C",
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      "name": "testRankList",
      "title": "testRankList",
      "object": "testRankList",
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      ],
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      "table": true,
      "tojson": true
    },
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      "name": "testTree",
      "title": "testTree",
      "object": "testTree",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
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      "title": "Internal Apoderoides Functions",
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        "calcOutScore_C",
        "deleteSubFunc",
        "extractOTUbyRankName_C",
        "findSubTips_C",
        "findUpperNode",
        "getAllCentroids_C",
        "getAllRankNames",
        "getRankCentroid_C",
        "getRankMRCA",
        "getTipNo_C",
        "is.monophyleticByRank"
      ]
    },
    {
      "page": "autoDeletion",
      "title": "autoDeletion",
      "topics": [
        "autoDeletion"
      ]
    },
    {
      "page": "calc.Score",
      "title": "calc.Score",
      "topics": [
        "calc.Score"
      ]
    },
    {
      "page": "deleteAnomaly",
      "title": "deleteAnomaly",
      "topics": [
        "deleteAnomaly"
      ]
    },
    {
      "page": "get.upperRank",
      "title": "get.upperRank",
      "topics": [
        "get.upperRank"
      ]
    },
    {
      "page": "getAllCentroids",
      "title": "getAllCentroids",
      "topics": [
        "getAllCentroids"
      ]
    },
    {
      "page": "getAllMRCAs",
      "title": "getAllMRCAs",
      "topics": [
        "getAllMRCAs"
      ]
    },
    {
      "page": "testRankList",
      "title": "testRankList",
      "topics": [
        "testRankList"
      ]
    },
    {
      "page": "testTree",
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    "digest",
    "lattice",
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      "headings": [
        "1 Aim of this package, Apoderoides",
        "2 Installation",
        "3 How to use",
        "3.1 Import a phylogenetic tree",
        "3.2 Score calculation",
        "3.2.1. Score at genus level",
        "3.2.2. Score at the other rank",
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        "3.4 The other utilities to help analysis"
      ],
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      "modified": "2024-07-10 05:33:21",
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