{
  "_id": "6a59bd9509eb0996dd68d41f",
  "Package": "EcoNiche",
  "Type": "Package",
  "Title": "Community Niche Position and Width Estimation Tools",
  "Version": "1.0.3",
  "Authors@R": "c(\nperson(\"Shuotao\", \"Zhou\", , \"zhoushuotao@stu.hunau.edu.cn\", role = c(\"aut\", \"cre\")),\nperson(\"Kai\", \"Feng\", , \"kaifeng@rcees.ac.cn\", role = \"aut\"),\nperson(\"Ye\", \"Deng\", , \"yedeng@rcees.ac.cn\", role = \"aut\")\n)",
  "Description": "Provides methods for estimating species niche position and\nniche breadth under continuous environmental gradients. The\npackage implements canonical correspondence analysis (CCA),\npartial CCA (pCCA), generalized additive models (GAM), and\nLevins' niche breadth metrics for species-level and\ncommunity-level analyses. Methods are based on ter Braak (1986)\n<doi:10.2307/1938672>, Okie et al. (2015)\n<doi:10.1098/rspb.2014.2630>, Feng et al. (2020)\n<doi:10.1111/mec.15441>, Wood (2017)\n<doi:10.1201/9781315370279>, and Levins (1968,\nISBN:978-0691080628).",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/yedeng-lab/EcoNiche",
  "BugReports": "https://github.com/yedeng-lab/EcoNiche/issues",
  "Repository": "https://yedeng-lab.r-universe.dev",
  "Date/Publication": "2026-06-17 02:16:37 UTC",
  "RemoteUrl": "https://github.com/yedeng-lab/econiche",
  "RemoteRef": "HEAD",
  "RemoteSha": "426786c88a5325d0a41fdd5abda05fc8b4e5d621",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-17 05:24:58 UTC",
    "User": "root"
  },
  "Author": "Shuotao Zhou [aut, cre],\nKai Feng [aut],\nYe Deng [aut]",
  "Maintainer": "Shuotao Zhou <zhoushuotao@stu.hunau.edu.cn>",
  "_user": "yedeng-lab",
  "_type": "src",
  "_file": "EcoNiche_1.0.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/04bcc3cf0b84389cc574b5f04556db84e1e8548a99190349b1568adfd6676006",
  "_filesize": 292838,
  "_sha256": "04bcc3cf0b84389cc574b5f04556db84e1e8548a99190349b1568adfd6676006",
  "_expires": "2026-10-25T05:28:52.000Z",
  "_created": "2026-07-17T05:24:58.000Z",
  "_published": "2026-07-17T05:28:53.896Z",
  "_jobs": [
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      "job": 87812053255,
      "time": 143,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8397931066"
    },
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      "config": "linux-release-x86_64",
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      "config": "windows-devel",
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      "config": "windows-oldrel",
      "r": "4.5.3",
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      "time": 70,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8397912232"
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  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/yedeng-lab/actions/runs/29557102751",
  "_status": "success",
  "_upstream": "https://github.com/yedeng-lab/econiche",
  "_commit": {
    "id": "426786c88a5325d0a41fdd5abda05fc8b4e5d621",
    "author": "zhoushuotao <1285792399@qq.com>",
    "committer": "zhoushuotao <1285792399@qq.com>",
    "message": "Fix CRAN availability information in README\n",
    "time": 1781662597
  },
  "_maintainer": {
    "name": "Shuotao Zhou",
    "email": "zhoushuotao@stu.hunau.edu.cn",
    "login": "zhoushuotao",
    "description": "",
    "uuid": 119387070
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "mgcv",
      "role": "Imports"
    },
    {
      "package": "vegan",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "viridisLite",
      "role": "Suggests"
    }
  ],
  "_owner": "yedeng-lab",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-09",
      "n": 7
    },
    {
      "week": "2026-10",
      "n": 4
    },
    {
      "week": "2026-25",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "zhoushuotao",
      "count": 16,
      "uuid": 119387070
    }
  ],
  "_userbio": {
    "uuid": 95005688,
    "type": "organization",
    "name": "Deng Lab",
    "followers": 23,
    "description": "Ye Deng's Lab for Metagenomics for Environmental Microbiology, from RCEES, CAS"
  },
  "_downloads": {
    "count": 245,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/EcoNiche"
  },
  "_devurl": "https://github.com/yedeng-lab/econiche",
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/EcoNiche.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/yedeng-lab/econiche",
  "_realowner": "yedeng-lab",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.2",
      "date": "2026-03-10"
    },
    {
      "version": "1.0.3",
      "date": "2026-06-16"
    }
  ],
  "_exports": [
    "cca_calc_gradient",
    "cca_calc_group",
    "cca_calc_species",
    "cca_fit_ordination",
    "cca_plot_group_env",
    "cca_prep_env",
    "cca_workflow",
    "cca_workflow_gradient",
    "cca_workflow_group",
    "gam_calc_sitewidth",
    "gam_fit_model",
    "gam_plot_species",
    "levins_calc_binned",
    "levins_calc_group",
    "levins_plot_pos_width",
    "niche_width_calc"
  ],
  "_datasets": [
    {
      "name": "plant_env",
      "title": "Example plant environmental table",
      "object": "plant_env",
      "class": [
        "data.frame"
      ],
      "fields": [
        "TN",
        "TK",
        "TP",
        "SOC",
        "AP",
        "AN",
        "Moisture",
        "AMT",
        "AMP",
        "pH",
        "abspH"
      ],
      "rows": 290,
      "table": true,
      "tojson": true
    },
    {
      "name": "plant_group",
      "title": "Example plant sample grouping",
      "object": "plant_group",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "plant_otu",
      "title": "Example plant community abundance table",
      "object": "plant_otu",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "DQS_DQS1",
        "DQS_DQS2",
        "DQS_DQS3",
        "DQS_DQS4",
        "DQS_DQS5",
        "DQS_DQS6",
        "DQS_DQS7",
        "DQS_DQS8",
        "DQS_DQS9",
        "DQS_DQS10",
        "LYW_LYW1",
        "LYW_LYW2",
        "LYW_LYW3",
        "LYW_LYW4",
        "LYW_LYW5",
        "LYW_LYW6",
        "LYW_LYW7",
        "LYW_LYW8",
        "LYW_LYW9",
        "LYW_LYW10",
        "PQG_PQG1",
        "PQG_PQG2",
        "PQG_PQG3",
        "PQG_PQG4",
        "PQG_PQG5",
        "PQG_PQG6",
        "PQG_PQG7",
        "PQG_PQG8",
        "PQG_PQG9",
        "PQG_PQG10",
        "HLS_HLS1",
        "HLS_HLS2",
        "HLS_HLS3",
        "HLS_HLS4",
        "HLS_HLS5",
        "HLS_HLS6",
        "HLS_HLS7",
        "HLS_HLS8",
        "HLS_HLS9",
        "HLS_HLS10",
        "LIS_LS1",
        "LIS_LS2",
        "LIS_LS3",
        "LIS_LS4",
        "LIS_LS5",
        "LIS_LS6",
        "LIS_LS7",
        "LIS_LS8",
        "LIS_LS9",
        "LIS_LS10",
        "MH_MH1",
        "MH_MH2",
        "MH_MH3",
        "MH_MH4",
        "MH_MH5",
        "MH_MH6",
        "MH_MH7",
        "MH_MH8",
        "MH_MH9",
        "MH_MH10",
        "XQL_XQL1",
        "XQL_XQL2",
        "XQL_XQL3",
        "XQL_XQL4",
        "XQL_XQL5",
        "XQL_XQL6",
        "XQL_XQL7",
        "XQL_XQL8",
        "XQL_XQL9",
        "XQL_XQL10",
        "BDGS_BDGS1",
        "BDGS_BDGS2",
        "BDGS_BDGS3",
        "BDGS_BDGS4",
        "BDGS_BDGS5",
        "BDGS_BDGS6",
        "BDGS_BDGS7",
        "BDGS_BDGS8",
        "BDGS_BDGS9",
        "BDGS_BDGS10",
        "NZ_NZ1",
        "NZ_NZ2",
        "NZ_NZ3",
        "NZ_NZ4",
        "NZ_NZ5",
        "NZ_NZ6",
        "NZ_NZ7",
        "NZ_NZ8",
        "NZ_NZ9",
        "NZ_NZ10",
        "BTM_BTM1",
        "BTM_BTM2",
        "BTM_BTM3",
        "BTM_BTM4",
        "BTM_BTM5",
        "BTM_BTM6",
        "BTM_BTM7",
        "BTM_BTM8",
        "BTM_BTM9",
        "BTM_BTM10",
        "SWD_SWD1",
        "SWD_SWD2",
        "SWD_SWD3",
        "SWD_SWD4",
        "SWD_SWD5",
        "SWD_SWD6",
        "SWD_SWD7",
        "SWD_SWD8",
        "SWD_SWD9",
        "SWD_SWD10",
        "DHY_DHY1",
        "DHY_DHY2",
        "DHY_DHY3",
        "DHY_DHY4",
        "DHY_DHY5",
        "DHY_DHY6",
        "DHY_DHY7",
        "DHY_DHY8",
        "DHY_DHY9",
        "DHY_DHY10",
        "SNJ_SNJ1",
        "SNJ_SNJ2",
        "SNJ_SNJ3",
        "SNJ_SNJ4",
        "SNJ_SNJ5",
        "SNJ_SNJ6",
        "SNJ_SNJ7",
        "SNJ_SNJ8",
        "SNJ_SNJ9",
        "SNJ_SNJ10",
        "BYS_BYS1",
        "BYS_BYS2",
        "BYS_BYS3",
        "BYS_BYS4",
        "BYS_BYS5",
        "BYS_BYS6",
        "BYS_BYS7",
        "BYS_BYS8",
        "BYS_BYS9",
        "BYS_BYS10",
        "DMS_DMS1",
        "DMS_DMS2",
        "DMS_DMS3",
        "DMS_DMS4",
        "DYS_DYS1",
        "DYS_DYS2",
        "DYS_DYS3",
        "DYS_DYS4",
        "DYS_DYS5",
        "DYS_DYS6",
        "DYS_DYS7",
        "DYS_DYS8",
        "DYS_DYS9",
        "DYS_DYS10",
        "FJS_FJS1",
        "FJS_FJS2",
        "FJS_FJS3",
        "FJS_FJS4",
        "FJS_FJS5",
        "FJS_FJS6",
        "FJS_FJS7",
        "FJS_FJS8",
        "FJS_FJS9",
        "FJS_FJS10",
        "GWJ_GWJ1",
        "GWJ_GWJ2",
        "GWJ_GWJ3",
        "GWJ_GWJ4",
        "GWJ_GWJ5",
        "GWJ_GWJ6",
        "GWJ_GWJ7",
        "GWJ_GWJ8",
        "GWJ_GWJ9",
        "GWJ_GWJ10",
        "HH_HH1",
        "HH_HH2",
        "HH_HH3",
        "HH_HH4",
        "HH_HH5",
        "HH_HH6",
        "HH_HH7",
        "HH_HH8",
        "HH_HH9",
        "HH_HH10",
        "HP_HP1",
        "HP_HP2",
        "HP_HP3",
        "HP_HP4",
        "HP_HP5",
        "HP_HP6",
        "HP_HP7",
        "HP_HP8",
        "HP_HP9",
        "HP_HP10",
        "HPS_HPS1",
        "HPS_HPS2",
        "HPS_HPS3",
        "HPS_HPS4",
        "HPS_HPS5",
        "HPS_HPS6",
        "HPS_HPS7",
        "HPS_HPS8",
        "HPS_HPS9",
        "HPS_HPS10",
        "HS_HS1",
        "HS_HS2",
        "HS_HS3",
        "HS_HS4",
        "HS_HS5",
        "HS_HS6",
        "HS_HS7",
        "HS_HS8",
        "HS_HS9",
        "HS_HS10",
        "LYS_LYS1",
        "LYS_LYS2",
        "LYS_LYS3",
        "LYS_LYS4",
        "LYS_LYS5",
        "LYS_LYS6",
        "LYS_LYS7",
        "LYS_LYS8",
        "LYS_LYS9",
        "LYS_LYS10",
        "MES_MES1",
        "MES_MES2",
        "MES_MES3",
        "MES_MES4",
        "MES_MES5",
        "MES_MES6",
        "MES_MES7",
        "MES_MES8",
        "MES_MES9",
        "MES_MES10",
        "WLS_WLS1",
        "WLS_WLS2",
        "WLS_WLS3",
        "WLS_WLS4",
        "WLS_WLS5",
        "WLS_WLS6",
        "MLZ_MLZ1",
        "MLZ_MLZ2",
        "MLZ_MLZ3",
        "MLZ_MLZ4",
        "MLZ_MLZ5",
        "MLZ_MLZ6",
        "MLZ_MLZ7",
        "MLZ_MLZ8",
        "MLZ_MLZ9",
        "MLZ_MLZ10",
        "MYH_MYH1",
        "MYH_MYH2",
        "MYH_MYH3",
        "MYH_MYH4",
        "MYH_MYH5",
        "MYH_MYH6",
        "MYH_MYH7",
        "MYH_MYH8",
        "MYH_MYH9",
        "MYH_MYH10",
        "JFL1_JFL1_1",
        "JFL1_JFL1_2",
        "JFL1_JFL1_3",
        "JFL1_JFL1_4",
        "JFL1_JFL1_5",
        "JFL1_JFL1_6",
        "JFL1_JFL1_7",
        "JFL1_JFL1_8",
        "JFL1_JFL1_9",
        "JFL1_JFL1_10",
        "JFL2_JFL2_1",
        "JFL2_JFL2_2",
        "JFL2_JFL2_3",
        "JFL2_JFL2_4",
        "JFL2_JFL2_5",
        "JFL2_JFL2_6",
        "JFL2_JFL2_7",
        "JFL2_JFL2_8",
        "JFL2_JFL2_9",
        "JFL2_JFL2_10",
        "JFL3_JFL3_1",
        "JFL3_JFL3_2",
        "JFL3_JFL3_3",
        "JFL3_JFL3_4",
        "JFL3_JFL3_5",
        "JFL3_JFL3_6",
        "JFL3_JFL3_7",
        "JFL3_JFL3_8",
        "JFL3_JFL3_9",
        "JFL3_JFL3_10"
      ],
      "rows": 1038,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "cca_calc_gradient",
      "title": "Plot Site Niche Position vs Environmental Gradient (Step 4)",
      "topics": [
        "cca_calc_gradient"
      ]
    },
    {
      "page": "cca_calc_group",
      "title": "Calculate Niche Width Summary by Group (Step 5)",
      "topics": [
        "cca_calc_group"
      ]
    },
    {
      "page": "cca_calc_species",
      "title": "Calculate Species Niche Width and Position (Step 3)",
      "topics": [
        "cca_calc_species"
      ]
    },
    {
      "page": "cca_fit_ordination",
      "title": "Fit CCA and Partial-CCA Ordination (Step 2)",
      "topics": [
        "cca_fit_ordination"
      ]
    },
    {
      "page": "cca_plot_group_env",
      "title": "Plot Sample/Group Niche Width vs Environmental Gradient (Step 6)",
      "topics": [
        "cca_plot_group_env"
      ]
    },
    {
      "page": "cca_prep_env",
      "title": "Prepare Environmental Data for CCA (Step 1)",
      "topics": [
        "cca_prep_env"
      ]
    },
    {
      "page": "cca_workflow",
      "title": "CCA-Based Niche Analysis Workflow Controller",
      "topics": [
        "cca_workflow"
      ]
    },
    {
      "page": "cca_workflow_gradient",
      "title": "Execute Gradient-Based Workflow (Steps 1-4)",
      "topics": [
        "cca_workflow_gradient"
      ]
    },
    {
      "page": "cca_workflow_group",
      "title": "Execute Group-Based Workflow (Steps 1-2, 5-6)",
      "topics": [
        "cca_workflow_group"
      ]
    },
    {
      "page": "gam_calc_sitewidth",
      "title": "Calculate Sample-Level Niche Width Weighted by Abundance",
      "topics": [
        "gam_calc_sitewidth"
      ]
    },
    {
      "page": "gam_fit_model",
      "title": "Fit GAM-Based Niche Curves for All OTUs",
      "topics": [
        "gam_fit_model"
      ]
    },
    {
      "page": "gam_plot_species",
      "title": "Plot GAM-Based Niche Curve for a Single OTU",
      "topics": [
        "gam_plot_species"
      ]
    },
    {
      "page": "levins_calc_binned",
      "title": "Calculate Levins Niche Width Along a Gradient (Binned States)",
      "topics": [
        "levins_calc_binned"
      ]
    },
    {
      "page": "levins_calc_group",
      "title": "Calculate Community-Mean Levins Niche Width Along a Gradient",
      "topics": [
        "levins_calc_group"
      ]
    },
    {
      "page": "levins_plot_pos_width",
      "title": "Plot Species Niche Position vs Levins Width",
      "topics": [
        "levins_plot_pos_width"
      ]
    },
    {
      "page": "niche_width_calc",
      "title": "Calculate Niche Width (Samples as States)",
      "topics": [
        "niche_width_calc"
      ]
    },
    {
      "page": "plant_env",
      "title": "Example plant environmental table",
      "topics": [
        "plant_env"
      ]
    },
    {
      "page": "plant_group",
      "title": "Example plant sample grouping",
      "topics": [
        "plant_group"
      ]
    },
    {
      "page": "plant_otu",
      "title": "Example plant community abundance table",
      "topics": [
        "plant_otu"
      ]
    }
  ],
  "_readme": "https://github.com/yedeng-lab/econiche/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cluster",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "MASS",
    "Matrix",
    "mgcv",
    "nlme",
    "permute",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "vegan",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "coniche-workflow.Rmd",
      "filename": "coniche-workflow.html",
      "title": "EcoNiche workflow",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Input data",
        "CCA / partial-CCA workflow",
        "Group-level workflow",
        "GAM response analysis",
        "Levins breadth along a binned gradient"
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