ordiresids: Plots of Residuals and Fitted Values for Constrained...

In vegan: Community Ecology Package

Description

The function provides plot.lm style diagnostic plots for the results of constrained ordination from cca, rda and capscale. Normally you do not need these plots, because ordination is descriptive and does not make assumptions on the distribution of the residuals. However, if you permute residuals in significance tests (anova.cca), you may be interested in inspecting that the residuals really are exchangeable and independent of fitted values.

Usage

ordiresids(x, kind = c("residuals", "scale", "qqmath"),
   residuals = "working", type = c("p", "smooth", "g"),
   formula, ...)

Arguments

x	Ordination result from cca, rda or capscale.
kind	The type of plot: "residuals" plot residuals against fitted values, "scale" the square root of absolute residuals against fitted values, and "qqmath" the residuals against expected distribution (defaults qnorm), unless defined differently in the formula argument).
residuals	The kind of residuals and fitted values. The argument is passed on to fitted.cca with alternatives "working" and "response".
type	The type of plot. The argument is passed on to lattice functions.
formula	Formula to override the default plot. The formula can contain items Fitted, Residuals, Species and Sites (provided that names of species and sites are available in the ordination result).
...	Other arguments passed to lattice functions.

Details

The default plots are similar as in plot.lm, but they use Lattice functions xyplot and qqmath. The alternatives have default formulae but these can be replaced by the user. The elements available in formula or in the groups argument are Fitted, Residuals, Species and Sites.

Value

The function return a Lattice object that can displayed as plot.

Author(s)

Jari Oksanen

See Also

plot.lm, Lattice, xyplot, qqmath.

Examples

data(varespec)
data(varechem)
mod <- cca(varespec ~ Al + P + K, varechem)
ordiresids(mod)

Example output

Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4

vegan documentation built on May 2, 2019, 5:51 p.m.