vegan (version 2.6-2)

tolerance: Species tolerances and sample heterogeneities

Description

Species tolerances and sample heterogeneities.

Usage

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

Value

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

Author

Gavin L. Simpson

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).

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)