{
  "_id": "6ae9e3b02e87f76f20ad10f2",
  "Package": "Nematode",
  "Title": "Ecological Indices Calculator for Nematode Communities",
  "Version": "0.3.2",
  "Date": "2026-10-04",
  "Authors@R": "c(\nperson(\"Yuxuan\", \"He\", , \"heyuxuan0525@outlook.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0007-1149-5554\")),\nperson(\"Dong\", \"Wang\", , \"wangdong19882005@163.com\", role = c(\"ths\")),\nperson(\"Yuan\", \"Miao\", , \"miaoyuan0921@126.com\", role = c(\"ths\"))\n)",
  "Description": "Provides a computational toolkit for analyzing nematode\ncommunities in ecological studies. Includes methods to quantify\nnematode-based ecological indicators such as metabolic\nfootprints, energy flow metrics, and community structure. These\ntools support assessments of soil health, ecosystem\nfunctioning, and trophic interactions, standardizing the use of\nnematodes as bioindicators.",
  "License": "GPL (>= 3)",
  "BuildManual": "no",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "Config/testthat/edition": "3",
  "RoxygenNote": "7.3.3",
  "Repository": "https://h-xuanjiu.r-universe.dev",
  "Date/Publication": "2026-10-04 14:37:54 UTC",
  "RemoteUrl": "https://github.com/h-xuanjiu/nematode",
  "RemoteRef": "HEAD",
  "RemoteSha": "bb97869eb6088ff35d8418a21b5ce415fcf5f923",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-03 13:32:13 UTC",
    "User": "root"
  },
  "Author": "Yuxuan He [aut, cre] (ORCID: <https://orcid.org/0009-0007-1149-5554>),\nDong Wang [ths],\nYuan Miao [ths]",
  "Maintainer": "Yuxuan He <heyuxuan0525@outlook.com>",
  "_user": "h-xuanjiu",
  "_type": "src",
  "_file": "Nematode_0.3.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/55d2450a33fa41d61fb468f73a058169a5d37bf952e89598b8db30d5bddbf607",
  "_filesize": 271633,
  "_sha256": "55d2450a33fa41d61fb468f73a058169a5d37bf952e89598b8db30d5bddbf607",
  "_expires": "2027-02-11T13:37:50.000Z",
  "_created": "2026-11-03T13:32:13.000Z",
  "_published": "2026-11-03T13:37:52.307Z",
  "_upstream": "https://github.com/h-xuanjiu/nematode",
  "_status": "success",
  "_maintainer": {
    "name": "Yuxuan He",
    "email": "heyuxuan0525@outlook.com",
    "login": "h-xuanjiu",
    "orcid": "0009-0007-1149-5554",
    "description": "",
    "uuid": 142601388
  },
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    "author": "h-xuanjiu <142601388+h-xuanjiu@users.noreply.github.com>",
    "committer": "h-xuanjiu <142601388+h-xuanjiu@users.noreply.github.com>",
    "message": "Fix missing functional guilds in SI and BI calculations.\n",
    "time": 1791124674
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  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
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      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
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      "package": "dplyr",
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      "version": ">= 3.0.0",
      "role": "Suggests"
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  "_owner": "h-xuanjiu",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "week": "2026-14",
      "n": 4
    },
    {
      "week": "2026-15",
      "n": 2
    },
    {
      "week": "2026-27",
      "n": 1
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  "_tags": [
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      "name": "v0.2.2",
      "date": "2026-04-02"
    },
    {
      "name": "v0.3.0",
      "date": "2026-04-07"
    },
    {
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      "date": "2026-07-03"
    },
    {
      "name": "v0.3.2",
      "date": "2026-10-04"
    }
  ],
  "_topics": [
    "nematode"
  ],
  "_stars": 2,
  "_contributors": [
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      "user": "h-xuanjiu",
      "count": 8,
      "uuid": 142601388
    }
  ],
  "_userbio": {
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    "type": "user",
    "name": "He-Yuxuan",
    "followers": 0
  },
  "_downloads": {
    "count": 414,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Nematode"
  },
  "_devurl": "https://github.com/h-xuanjiu/nematode",
  "_searchresults": 0,
  "_rbuild": "4.6.2",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/Nematode.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/h-xuanjiu/nematode",
  "_realowner": "h-xuanjiu",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.2.0",
      "date": "2025-08-20"
    },
    {
      "version": "0.2.1",
      "date": "2025-09-07"
    },
    {
      "version": "0.2.2",
      "date": "2026-03-19"
    },
    {
      "version": "0.3.0",
      "date": "2026-04-07"
    },
    {
      "version": "0.3.1",
      "date": "2026-07-12"
    },
    {
      "version": "0.3.2",
      "date": "2026-10-04"
    }
  ],
  "_exports": [
    "cal.BI",
    "cal.CI",
    "cal.EI",
    "cal.H",
    "cal.J",
    "cal.MI",
    "cal.NCR",
    "cal.PPI",
    "cal.SI",
    "cal.Simpson",
    "cal.SRI",
    "cal.TD",
    "cal.WI",
    "check_nematode_genus",
    "cp_rel_abundance",
    "diet_rel_abundance",
    "Ecological.Indices",
    "fuzzy_genus_match",
    "NEF",
    "NMF",
    "num_species",
    "rel_abundance",
    "runNMDS",
    "runPCoA",
    "runSimper"
  ],
  "_datasets": [
    {
      "name": "nematode.ave.mass",
      "title": "Nematode Genus and Family Average Body Mass",
      "object": "nematode.ave.mass",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Genus",
        "Family",
        "Genus.Average.Mass",
        "Family.Average.Mass"
      ],
      "rows": 1094,
      "table": true,
      "tojson": true
    },
    {
      "name": "nematode.info",
      "title": "Nematode Taxonomic and Functional Traits",
      "object": "nematode.info",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Genus",
        "Family",
        "Feeding_habit",
        "CP_group"
      ],
      "rows": 2524,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "cal.BI",
      "title": "Calculate Basic Index (BI)",
      "topics": [
        "cal.BI",
        "cal.BI.data.frame",
        "cal.BI.default",
        "cal.BI.matrix"
      ]
    },
    {
      "page": "cal.CI",
      "title": "Calculate Channel Index (CI)",
      "topics": [
        "cal.CI",
        "cal.CI.data.frame",
        "cal.CI.default",
        "cal.CI.matrix"
      ]
    },
    {
      "page": "cal.EI",
      "title": "Calculate Enrichment Index (EI)",
      "topics": [
        "cal.EI",
        "cal.EI.data.frame",
        "cal.EI.default",
        "cal.EI.matrix"
      ]
    },
    {
      "page": "cal.H",
      "title": "Calculate Shannon-Wiener Index (H)",
      "topics": [
        "cal.H",
        "cal.H.data.frame",
        "cal.H.default",
        "cal.H.matrix"
      ]
    },
    {
      "page": "cal.J",
      "title": "Calculate Pielou's Evenness Index (J)",
      "topics": [
        "cal.J",
        "cal.J.data.frame",
        "cal.J.default",
        "cal.J.matrix"
      ]
    },
    {
      "page": "cal.MI",
      "title": "Calculate Maturity Index (MI)",
      "topics": [
        "cal.MI",
        "cal.MI.data.frame",
        "cal.MI.default",
        "cal.MI.matrix"
      ]
    },
    {
      "page": "cal.NCR",
      "title": "Calculate Nematode Channel Ratio (NCR)",
      "topics": [
        "cal.NCR",
        "cal.NCR.data.frame",
        "cal.NCR.default",
        "cal.NCR.matrix"
      ]
    },
    {
      "page": "cal.PPI",
      "title": "Calculate Plant Parasite Index (PPI)",
      "topics": [
        "cal.PPI",
        "cal.PPI.data.frame",
        "cal.PPI.default",
        "cal.PPI.matrix"
      ]
    },
    {
      "page": "cal.SI",
      "title": "Calculate Structure Index (SI)",
      "topics": [
        "cal.SI",
        "cal.SI.data.frame",
        "cal.SI.default",
        "cal.SI.matrix"
      ]
    },
    {
      "page": "cal.Simpson",
      "title": "Calculate Simpson Index",
      "topics": [
        "cal.Simpson",
        "cal.Simpson.data.frame",
        "cal.Simpson.default",
        "cal.Simpson.matrix"
      ]
    },
    {
      "page": "cal.SRI",
      "title": "Calculate Species Richness Index (SRI)",
      "topics": [
        "cal.SRI",
        "cal.SRI.data.frame",
        "cal.SRI.default",
        "cal.SRI.matrix"
      ]
    },
    {
      "page": "cal.TD",
      "title": "Calculate Trophic Diversity (TD) Index",
      "topics": [
        "cal.TD",
        "cal.TD.data.frame",
        "cal.TD.default",
        "cal.TD.matrix"
      ]
    },
    {
      "page": "cal.WI",
      "title": "Calculate Wasilewska Index (WI)",
      "topics": [
        "cal.WI",
        "cal.WI.data.frame",
        "cal.WI.default",
        "cal.WI.matrix"
      ]
    },
    {
      "page": "check_nematode_genus",
      "title": "Check validity of nematode genus names against reference database",
      "topics": [
        "check_nematode_genus",
        "check_nematode_genus.character",
        "check_nematode_genus.data.frame",
        "check_nematode_genus.default"
      ]
    },
    {
      "page": "cp_rel_abundance",
      "title": "Calculate CP Relative or Absolute Abundance",
      "topics": [
        "cp_rel_abundance",
        "cp_rel_abundance.data.frame",
        "cp_rel_abundance.default",
        "cp_rel_abundance.matrix"
      ]
    },
    {
      "page": "diet_rel_abundance",
      "title": "Calculate Diet Relative or Absolute Abundance",
      "topics": [
        "diet_rel_abundance",
        "diet_rel_abundance.data.frame",
        "diet_rel_abundance.default",
        "diet_rel_abundance.matrix"
      ]
    },
    {
      "page": "Ecological.Indices",
      "title": "Calculate Ecological Indices of Nematodes",
      "topics": [
        "Ecological.Indices",
        "Ecological.Indices.data.frame",
        "Ecological.Indices.default",
        "Ecological.Indices.matrix"
      ]
    },
    {
      "page": "fuzzy_genus_match",
      "title": "Fuzzy Matching of Nematode Genus Names",
      "topics": [
        "fuzzy_genus_match"
      ]
    },
    {
      "page": "NEF",
      "title": "Nematode Energy Footprints (NEF) Calculation",
      "topics": [
        "NEF",
        "NEF.data.frame",
        "NEF.default",
        "NEF.matrix"
      ]
    },
    {
      "page": "nematode.ave.mass",
      "title": "Nematode Genus and Family Average Body Mass",
      "topics": [
        "nematode.ave.mass"
      ]
    },
    {
      "page": "nematode.info",
      "title": "Nematode Taxonomic and Functional Traits",
      "topics": [
        "nematode.info"
      ]
    },
    {
      "page": "NMF",
      "title": "Nematode Metabolic Footprints (NMF) Calculation",
      "topics": [
        "NMF",
        "NMF.data.frame",
        "NMF.default",
        "NMF.matrix"
      ]
    },
    {
      "page": "num_species",
      "title": "Calculate Number of Species",
      "topics": [
        "num_species",
        "num_species.data.frame",
        "num_species.default",
        "num_species.matrix"
      ]
    },
    {
      "page": "rel_abundance",
      "title": "Calculate the Relative Abundance of Nematodes",
      "topics": [
        "rel_abundance",
        "rel_abundance.data.frame",
        "rel_abundance.default",
        "rel_abundance.matrix"
      ]
    },
    {
      "page": "runNMDS",
      "title": "Non-Metric Multidimensional Scaling (NMDS) Analysis",
      "topics": [
        "runNMDS",
        "runNMDS.data.frame",
        "runNMDS.default",
        "runNMDS.matrix"
      ]
    },
    {
      "page": "runPCoA",
      "title": "Principal Coordinates Analysis (PCoA) Analysis",
      "topics": [
        "runPCoA",
        "runPCoA.data.frame",
        "runPCoA.default",
        "runPCoA.matrix"
      ]
    },
    {
      "page": "runSimper",
      "title": "Similarity Percentages Analysis",
      "topics": [
        "runSimper",
        "runSimper.default",
        "runSimper.Ordination"
      ]
    },
    {
      "page": "summary",
      "title": "Summarize NMDS Results",
      "topics": [
        "summary.NMDS",
        "summary.PCoA"
      ]
    }
  ],
  "_readme": "https://github.com/h-xuanjiu/nematode/raw/HEAD/README.md",
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  "_score": 3.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "nematode",
  "_universes": [
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