tolerance: Species tolerances and sample heterogeneities

In pattakosn/Rworkshop: Community Ecology Package

Description

Species tolerances and sample heterogeneities.

Usage

tolerance(x, ...)

## S3 method for class 'cca'
tolerance(x, choices = 1:2, which = c("species","sites"),
    scaling = 2, useN2 = 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	numeric; the ordination scaling to use.
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.

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)

pattakosn/Rworkshop documentation built on May 24, 2019, 8:22 p.m.