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

ordiresids {vegan} | R Documentation

## 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. 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)

[Package vegan version 2.4-3 Index]