goodness.metaMDS {vegan} | R Documentation |

## Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling

### Description

Function `goodness.metaMDS`

find goodness of fit measure for
points in nonmetric multidimensional scaling, and function
`stressplot`

makes a `Shepard`

diagram.

### Usage

## S3 method for class 'metaMDS':
goodness(object, dis, ...)
stressplot(object, dis, pch, p.col = "blue", l.col = "red", lwd = 2,
...)

### Arguments

`object` |
A result object from `metaMDS` or
`isoMDS` . |

`dis` |
Dissimilarities. Normally this should not used with
`metaMDS` , but should be always used with
`isoMDS` . |

`pch` |
Plotting character for points. Default is dependent on the
number of points. |

`p.col, l.col` |
Point and line colours. |

`lwd` |
Line width. |

`...` |
Other parameters to functions, e.g. graphical parameters. |

### Details

Function `goodness.metaMDS`

finds a goodness of fit statistic for
observations (points). This is defined so that sum of squared values
is equal to squared stress. Large values indicate poor fit.

Function `stressplot`

is a wrapper to `Shepard`

function in MASS package. It plots ordination distances
against original dissimilarities, and draws a step line of the
nonlinear fit. In addition, it adds to the graph two correlation-like
statistics on the goodness of fit. The nonmetric fit is based on stress *S* and
defined as *sqrt(1-S^2)*. The “linear fit”
is the correlation between fitted values and ordination distances.

Both functions can be used both with `metaMDS`

and with
`isoMDS`

. With `metaMDS`

, the functions
try to reconstruct the dissimilarities using
`metaMDSredist`

, and dissimilarities should not be given.
With `isoMDS`

the dissimilarities must be given.
In either case, the functions inspect that dissimilarities are
consistent with current ordination, and refuse to analyse inconsistent
dissimilarities. Function `goodness.metaMDS`

is generic in
`vegan`

, but you must spell its name completely with
`isoMDS`

which has no class.

### Value

Function `goodness`

returns a vector of values. Function
`stressplot`

returns invisibly a `Shepard`

object.

### Author(s)

Jari Oksanen.

### See Also

`metaMDS`

, `isoMDS`

,
`Shepard`

.

### Examples

data(varespec)
mod <- metaMDS(varespec)
stressplot(mod)
gof <- goodness(mod)
gof
plot(mod, display = "sites", type = "n")
points(mod, display = "sites", cex = gof/2)

[Package

*vegan* version 1.16-32

Index]