vegan: ordiresids – R documentation

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ordiresids

Plots of Residuals and Fitted Values for Constrained Ordination

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, with alternatives `"working"`, `"response"`, `"standardized"` and `"studentized"` (see Details).
`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.

With residuals = "response" and residuals = "working" the fitted values and residuals are found with functions fitted.cca and residuals.cca. With residuals = "standardized" the residuals are found with rstandard.cca, and with residuals = "studentized" they are found with rstudent.cca, and in both cases the fitted values are standardized with sigma.cca.

Value

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

Author(s)

Jari Oksanen

Examples

data(varespec)
data(varechem)
mod <- cca(varespec ~ Al + P + K, varechem)
ordiresids(mod)
ordiresids(mod, formula = Residuals ~ Fitted | Species, residuals="standard",
   cex = 0.5)

vegan

Community Ecology Package

v2.5-7

GPL-2

Authors

Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs, Helene Wagner

Initial release