R: Species tolerances and sample heterogeneities

tolerance {vegan} | R Documentation

## Species tolerances and sample heterogeneities

### Description

Species tolerances and sample heterogeneities.

### Usage

    tolerance(x, ...)

    ## S3 method for class 'cca'
    tolerance(x, choices = 1:2, which = c("species","sites"),
              scaling = "species", useN2 = TRUE, hill = FALSE, ...)

### Arguments

`x` | object of class `"cca"`.
`choices` | numeric; which ordination axes to compute tolerances and heterogeneities for. Defaults to axes 1 and 2.
`which` | character; one of `"species"` or `"sites"`, indicating whether species tolerances or sample heterogeneities respectively are computed.
`scaling` | character or numeric; the ordination scaling to use. See `scores.cca` for details.
`hill` | logical; if `scaling` is a character, these control whether Hill's scaling is used for (C)CA respectively. See `scores.cca` for details.
`useN2` | logical; should the bias in the tolerances / heterogeneities be reduced via scaling by Hill's N2?
`...` | arguments passed to other methods.

### Details

Function to compute species tolerances and site heterogeneity measures from unimodal ordinations (CCA & CA). Implements Eq 6.47 and 6.48 from the Canoco 4.5 Reference Manual (pages 178–179).

### Value

Matrix of tolerances/heterogeneities with some additional attributes: `which`, `scaling`, and `N2`, the latter of which will be `NA` if `useN2 = FALSE`.

### Author(s)

Gavin L. Simpson

### Examples

    data(dune)
    data(dune.env)
    mod <- cca(dune ~ ., data = dune.env)

    ## defaults to species tolerances
    tolerance(mod)

    ## sample heterogeneities for CCA axes 1:6
    tolerance(mod, which = "sites", choices = 1:6)

[Package vegan version 2.4-3 Index]