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 1.16-32

Index]