{
  "name": "vegan R package: core functions, the research question each answers and their documented signatures",
  "description": "Compiled from the vegan reference pages on the package development site: for six core functions, the ecological question it answers and the default signature as documented in version 2.8-0 of the reference.",
  "page": "https://casrai.org/guides/vegan-r-package",
  "publisher": "CASRAI",
  "license": "https://creativecommons.org/licenses/by/4.0/",
  "dateModified": "2026-11-14T20:24:22Z",
  "temporalCoverage": "2026",
  "spatialCoverage": null,
  "columns": [
    {
      "name": "Function",
      "unit": "",
      "description": ""
    },
    {
      "name": "Question it answers",
      "unit": "",
      "description": ""
    },
    {
      "name": "Documented signature (defaults)",
      "unit": "",
      "description": ""
    },
    {
      "name": "Reference page",
      "unit": "",
      "description": ""
    }
  ],
  "rows": [
    {
      "Function": "diversity()",
      "Question it answers": "How diverse is each site?",
      "Documented signature (defaults)": "diversity(x, index = \"shannon\", groups, equalize.groups = FALSE, MARGIN = 1, base = exp(1))",
      "Reference page": "https://vegandevs.github.io/vegan/reference/diversity.html"
    },
    {
      "Function": "specnumber()",
      "Question it answers": "How many species per site or group?",
      "Documented signature (defaults)": "specnumber(x, groups, MARGIN = 1)",
      "Reference page": "https://vegandevs.github.io/vegan/reference/diversity.html"
    },
    {
      "Function": "rarefy()",
      "Question it answers": "What richness is expected in a random subsample of counts?",
      "Documented signature (defaults)": "rarefy(x, sample, se = FALSE, MARGIN = 1)",
      "Reference page": "https://vegandevs.github.io/vegan/reference/rarefy.html"
    },
    {
      "Function": "metaMDS()",
      "Question it answers": "Which sites have similar composition (NMDS)?",
      "Documented signature (defaults)": "metaMDS(comm, distance = \"bray\", k = 2, try = 20, trymax = 20, engine = monoMDS, autotransform = TRUE, noshare = FALSE, wascores = TRUE, ...)",
      "Reference page": "https://vegandevs.github.io/vegan/reference/metaMDS.html"
    },
    {
      "Function": "adonis2()",
      "Question it answers": "Does composition differ among groups or along predictors (PERMANOVA)?",
      "Documented signature (defaults)": "adonis2(formula, data, permutations = 999, method = \"bray\", sqrt.dist = FALSE, add = FALSE, by = NULL, ...)",
      "Reference page": "https://vegandevs.github.io/vegan/reference/adonis.html"
    },
    {
      "Function": "envfit()",
      "Question it answers": "Which environmental variables align with the ordination?",
      "Documented signature (defaults)": "envfit(ord, env, permutations = 999, strata = NULL, choices = c(1,2), display = \"sites\", w, na.rm = FALSE, ...)",
      "Reference page": "https://vegandevs.github.io/vegan/reference/envfit.html"
    }
  ],
  "sources": [
    {
      "title": "vegan reference index (vegandevs.github.io)",
      "url": "https://vegandevs.github.io/vegan/",
      "accessed": "2026-11-14"
    },
    {
      "title": "vegan: Community Ecology Package (CRAN)",
      "url": "https://cran.r-project.org/web/packages/vegan/index.html",
      "accessed": "2026-11-14"
    }
  ]
}