{
  "_id": "6a12c1d8acfb0bcc41d1e1c3",
  "Package": "easynem",
  "Title": "Nematode Community Analysis",
  "Version": "1.0.3",
  "Authors@R": "person(\"Wang\", \"Kunguang\", , \"whkygl@163.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7384-5002\"))",
  "Description": "Provides a built-in Nemaplex database for nematodes, which\ncan be used to search for various nematodes. Also supports\nvarious nematode community and functional analyses such as\nnematode diversity, maturity index, metabolic footprint, and\nfunctional guild. The methods are based on\n<https://shiny.wur.nl/ninja/>, Bongers, T. (1990)\n<doi:10.1007/BF00324627>, Ferris, H. (2010)\n<doi:10.1016/j.ejsobi.2010.01.003>, Wan, B. et al. (2022)\n<doi:10.1016/j.soilbio.2022.108695>, and Van Den Hoogen, J. et\nal. (2019) <doi:10.1038/s41586-019-1418-6>.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "LazyData": "true",
  "Config/testthat/edition": "3",
  "Language": "en-US",
  "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibglpk-dev make libicu-dev libuv1-dev libxml2-dev libx11-dev\nzlib1g-dev",
  "Repository": "https://whkygl.r-universe.dev",
  "Date/Publication": "2025-11-24 14:07:36 UTC",
  "RemoteUrl": "https://github.com/whkygl/easynem",
  "RemoteRef": "HEAD",
  "RemoteSha": "e0c5215144885488f3253779d0672c173bd68fc5",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-24 09:11:28 UTC",
    "User": "root"
  },
  "Author": "Wang Kunguang [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-7384-5002>)",
  "Maintainer": "Wang Kunguang <whkygl@163.com>",
  "MD5sum": "b9c5c9cdde51e2605538390985a9a6e7",
  "_user": "whkygl",
  "_type": "src",
  "_file": "easynem_1.0.3.tar.gz",
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  "_created": "2026-05-24T09:11:28.000Z",
  "_published": "2026-05-24T09:16:08.416Z",
  "_distro": "noble",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/whkygl/actions/runs/26357153328",
  "_status": "success",
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  "_upstream": "https://github.com/whkygl/easynem",
  "_commit": {
    "id": "e0c5215144885488f3253779d0672c173bd68fc5",
    "author": "Kunguang Wang <whkygl@163.com>",
    "committer": "Kunguang Wang <whkygl@163.com>",
    "message": "Fix KruskalTest\n",
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    "name": "Wang Kunguang",
    "email": "whkygl@163.com",
    "login": "whkygl",
    "description": "",
    "uuid": 71704250,
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  "_selfowned": true,
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  "_devurl": "https://github.com/whkygl/easynem",
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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    "extra/contents.json",
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  "_homeurl": "https://github.com/whkygl/easynem",
  "_realowner": "whkygl",
  "_cranurl": true,
  "_releases": [
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      "date": "2025-10-28"
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  "_exports": [
    "calc_alpha",
    "calc_beta",
    "calc_beta2",
    "calc_compare",
    "calc_compare2",
    "calc_ef",
    "calc_ef2",
    "calc_funguild",
    "calc_funguild2",
    "calc_lm",
    "calc_lm2",
    "calc_mf",
    "calc_mf2",
    "calc_nemindex",
    "calc_ter",
    "calc_ter2",
    "easynem_example",
    "filter_name",
    "filter_num",
    "geom_encircle",
    "HSD",
    "HSD2",
    "KruskalTest",
    "KruskalTest2",
    "LSD",
    "LSD2",
    "nem_calc",
    "nem_database",
    "nem_plot",
    "nem_trans",
    "order_factor",
    "read_nem",
    "read_nem2",
    "trans_combine",
    "trans_formula",
    "trans_formula_v",
    "trans_name",
    "trans_norm",
    "trans_rare",
    "TTest",
    "TTest2",
    "WilcoxTest",
    "WilcoxTest2"
  ],
  "_datasets": [
    {
      "name": "nemmeta",
      "title": "Experimental Design of Kiwifruit Cover Crops",
      "object": "nemmeta",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "SampleID",
        "Treatments"
      ],
      "rows": 12,
      "table": true,
      "tojson": true
    },
    {
      "name": "nemtab",
      "title": "Table of soil nematode abundance in kiwifruit orchards",
      "object": "nemtab",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "OTUID",
        "CK_1",
        "CK_2",
        "CK_3",
        "C2_1",
        "C2_2",
        "C2_3",
        "C4_1",
        "C4_2",
        "C4_3",
        "C8_1",
        "C8_2",
        "C8_3"
      ],
      "rows": 46,
      "table": true,
      "tojson": true
    },
    {
      "name": "nemtax",
      "title": "Nematode taxonomy table",
      "object": "nemtax",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "OTUID",
        "Kingdom",
        "Phylum",
        "Family",
        "Genus"
      ],
      "rows": 46,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "alpha-class",
      "title": "Class for storing alpha diversity calculation results",
      "topics": [
        "alpha-class"
      ]
    },
    {
      "page": "beta-class",
      "title": "A class to store beta diversity results (single factor)",
      "topics": [
        "beta-class"
      ]
    },
    {
      "page": "beta2-class",
      "title": "A class to store beta diversity results (two-factor)",
      "topics": [
        "beta2-class"
      ]
    },
    {
      "page": "calc_alpha",
      "title": "Alpha diversity analysis, generating alpha-class",
      "topics": [
        "calc_alpha"
      ]
    },
    {
      "page": "calc_beta",
      "title": "Beta diversity analysis, generating beta-class (single factor)",
      "topics": [
        "calc_beta"
      ]
    },
    {
      "page": "calc_beta2",
      "title": "Beta diversity analysis, generating beta2-class (two-factor)",
      "topics": [
        "calc_beta2"
      ]
    },
    {
      "page": "calc_compare",
      "title": "Multiple comparisons between treatments (single factor)",
      "topics": [
        "calc_compare"
      ]
    },
    {
      "page": "calc_compare2",
      "title": "Multiple comparisons between treatments (two-factor)",
      "topics": [
        "calc_compare2"
      ]
    },
    {
      "page": "calc_ef",
      "title": "Calculation of energy flow in nematode communities (single factor)",
      "topics": [
        "calc_ef"
      ]
    },
    {
      "page": "calc_ef2",
      "title": "Calculation of energy flow in nematode communities (two-factor)",
      "topics": [
        "calc_ef2"
      ]
    },
    {
      "page": "calc_funguild",
      "title": "Nematode food web analysis (single factor)",
      "topics": [
        "calc_funguild"
      ]
    },
    {
      "page": "calc_funguild2",
      "title": "Nematode food web analysis (two-factor)",
      "topics": [
        "calc_funguild2"
      ]
    },
    {
      "page": "calc_lm",
      "title": "Linear regression analysis of easynem-class (single factor)",
      "topics": [
        "calc_lm"
      ]
    },
    {
      "page": "calc_lm2",
      "title": "Linear regression analysis of easynem-class (two-factor)",
      "topics": [
        "calc_lm2"
      ]
    },
    {
      "page": "calc_mf",
      "title": "Calculating the metabolic footprint of nematodes (single factor)",
      "topics": [
        "calc_mf"
      ]
    },
    {
      "page": "calc_mf2",
      "title": "Calculating the metabolic footprint of nematodes (two-factor)",
      "topics": [
        "calc_mf2"
      ]
    },
    {
      "page": "calc_nemindex",
      "title": "Calculate multiple nematode ecological indices and generate nemindex class",
      "topics": [
        "calc_nemindex"
      ]
    },
    {
      "page": "calc_ter",
      "title": "Trivariate analysis of nematode feeding or cp value (single factor)",
      "topics": [
        "calc_ter"
      ]
    },
    {
      "page": "calc_ter2",
      "title": "Trivariate analysis of nematode feeding or cp value (two-factor)",
      "topics": [
        "calc_ter2"
      ]
    },
    {
      "page": "compare-class",
      "title": "A S4 class to store multiple comparisons results (single factor).",
      "topics": [
        "compare-class"
      ]
    },
    {
      "page": "compare2-class",
      "title": "A S4 class to store multiple comparisons results (two-factor).",
      "topics": [
        "compare2-class"
      ]
    },
    {
      "page": "easynem_example",
      "title": "Path to example files",
      "topics": [
        "easynem_example"
      ]
    },
    {
      "page": "easynem-class",
      "title": "The main experiment-level class for easynem data",
      "topics": [
        "easynem-class"
      ]
    },
    {
      "page": "ef-class",
      "title": "A S4 class to store energy flow results (single factor)",
      "topics": [
        "ef-class"
      ]
    },
    {
      "page": "ef2-class",
      "title": "A S4 class to store energy flow results (two-factor)",
      "topics": [
        "ef2-class"
      ]
    },
    {
      "page": "filter_name",
      "title": "Filter easynem by column name and keep rows that match a condition",
      "topics": [
        "filter_name"
      ]
    },
    {
      "page": "filter_num",
      "title": "Filter easynem's tab by discovery rate or abundance",
      "topics": [
        "filter_num"
      ]
    },
    {
      "page": "funguild-class",
      "title": "Class for storing computational results of nematode functional guild analysis (single factor)",
      "topics": [
        "funguild-class"
      ]
    },
    {
      "page": "funguild2-class",
      "title": "Class for storing computational results of nematode functional guild analysis (two-factor)",
      "topics": [
        "funguild2-class"
      ]
    },
    {
      "page": "geom_encircle",
      "title": "Automatically enclose points in a polygon",
      "topics": [
        "geom_encircle"
      ]
    },
    {
      "page": "HSD",
      "title": "Compute Tukey Honest Significant Differences (single factor)",
      "topics": [
        "HSD"
      ]
    },
    {
      "page": "HSD2",
      "title": "Compute Tukey Honest Significant Differences (two-factor)",
      "topics": [
        "HSD2"
      ]
    },
    {
      "page": "KruskalTest",
      "title": "Perform Kruskal-Wallis test on easynem meta-table by treatment (single factor)",
      "topics": [
        "KruskalTest"
      ]
    },
    {
      "page": "KruskalTest2",
      "title": "Perform Kruskal-Wallis test on easynem meta-table by treatment (two-factor)",
      "topics": [
        "KruskalTest2"
      ]
    },
    {
      "page": "lme-class",
      "title": "A S4 class to store the linear regression analysis results (single factor)",
      "topics": [
        "lme-class"
      ]
    },
    {
      "page": "lme2-class",
      "title": "A S4 class to store the linear regression analysis results (two-factor)",
      "topics": [
        "lme2-class"
      ]
    },
    {
      "page": "LSD",
      "title": "Multiple comparisons, \"Least significant difference\" and Adjust P-values (single factor)",
      "topics": [
        "LSD"
      ]
    },
    {
      "page": "LSD2",
      "title": "Multiple comparisons, \"Least significant difference\" and Adjust P-values (two-factor)",
      "topics": [
        "LSD2"
      ]
    },
    {
      "page": "mf-class",
      "title": "A S4 class to store Metabolic footprints results (single factor)",
      "topics": [
        "mf-class"
      ]
    },
    {
      "page": "mf2-class",
      "title": "A S4 class to store Metabolic footprints results (two-factor)",
      "topics": [
        "mf2-class"
      ]
    },
    {
      "page": "nem_calc",
      "title": "calc",
      "topics": [
        "nem_calc"
      ]
    },
    {
      "page": "nem_database",
      "title": "Nematode database search",
      "topics": [
        "nem_database"
      ]
    },
    {
      "page": "nem_plot",
      "title": "Visualize the results of the calculation",
      "topics": [
        "nem_plot"
      ]
    },
    {
      "page": "nem_plot-beta-method",
      "title": "Visualization of beta diversity results (single factor)",
      "topics": [
        "nem_plot,beta-method"
      ]
    },
    {
      "page": "nem_plot-beta2-method",
      "title": "Visualization of beta diversity results (two-factor)",
      "topics": [
        "nem_plot,beta2-method"
      ]
    },
    {
      "page": "nem_plot-compare-method",
      "title": "Visualizing the results of multiple comparisons (single factor)",
      "topics": [
        "nem_plot,compare-method"
      ]
    },
    {
      "page": "nem_plot-compare2-method",
      "title": "Visualizing the results of multiple comparisons (two-factor)",
      "topics": [
        "nem_plot,compare2-method"
      ]
    },
    {
      "page": "nem_plot-ef-method",
      "title": "Visualizing the energy structure of nematode communities (single factor)",
      "topics": [
        "nem_plot,ef-method"
      ]
    },
    {
      "page": "nem_plot-ef2-method",
      "title": "Visualizing the energy structure of nematode communities (two-factor)",
      "topics": [
        "nem_plot,ef2-method"
      ]
    },
    {
      "page": "nem_plot-funguild-method",
      "title": "Visualizing nematode functional guild data (single factor)",
      "topics": [
        "nem_plot,funguild-method"
      ]
    },
    {
      "page": "nem_plot-funguild2-method",
      "title": "Visualizing nematode functional guild data (two-factor)",
      "topics": [
        "nem_plot,funguild2-method"
      ]
    },
    {
      "page": "nem_plot-lme-method",
      "title": "Visualizing the results of linear regression (single factor)",
      "topics": [
        "nem_plot,lme-method"
      ]
    },
    {
      "page": "nem_plot-lme2-method",
      "title": "Visualizing the results of linear regression (two-factor)",
      "topics": [
        "nem_plot,lme2-method"
      ]
    },
    {
      "page": "nem_plot-mf-method",
      "title": "Visualizing the metabolic footprint of nematode communities (single factor)",
      "topics": [
        "nem_plot,mf-method"
      ]
    },
    {
      "page": "nem_plot-mf2-method",
      "title": "Visualizing the metabolic footprint of nematode communities (two-factor)",
      "topics": [
        "nem_plot,mf2-method"
      ]
    },
    {
      "page": "nem_plot-ter-method",
      "title": "Visualizing the results of the ternary analysis (single factor)",
      "topics": [
        "nem_plot,ter-method"
      ]
    },
    {
      "page": "nem_plot-ter2-method",
      "title": "Visualizing the results of the ternary analysis (two-factor)",
      "topics": [
        "nem_plot,ter2-method"
      ]
    },
    {
      "page": "nem_trans",
      "title": "nem_trans",
      "topics": [
        "nem_trans"
      ]
    },
    {
      "page": "nemindex-class",
      "title": "Class for storing nematode ecological index calculation results",
      "topics": [
        "nemindex-class"
      ]
    },
    {
      "page": "nemmeta",
      "title": "Experimental Design of Kiwifruit Cover Crops",
      "topics": [
        "nemmeta"
      ]
    },
    {
      "page": "nemtab",
      "title": "Table of soil nematode abundance in kiwifruit orchards",
      "topics": [
        "nemtab"
      ]
    },
    {
      "page": "nemtax",
      "title": "Nematode taxonomy table",
      "topics": [
        "nemtax"
      ]
    },
    {
      "page": "order_factor",
      "title": "order_factor",
      "topics": [
        "order_factor"
      ]
    },
    {
      "page": "read_nem",
      "title": "Build easynem-class objects from their csv file",
      "topics": [
        "read_nem"
      ]
    },
    {
      "page": "read_nem2",
      "title": "Build easynem-class objects from their tibble type object",
      "topics": [
        "read_nem2"
      ]
    },
    {
      "page": "ter-class",
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