Description Usage Arguments Details Value Author(s) See Also Examples

Functions plot ordination distances in given number of dimensions
against observed distances or distances in full space in eigenvector
methods. The display is similar as the Shepard diagram
(`stressplot`

for non-metric multidimensional scaling
with `metaMDS`

or `monoMDS`

), but shows the
linear relationship of the eigenvector ordinations. The
`stressplot`

methods are available for `wcmdscale`

,
`rda`

, `cca`

, `capscale`

,
`dbrda`

, `prcomp`

and `princomp`

.

1 2 3 | ```
## S3 method for class 'wcmdscale'
stressplot(object, k = 2, pch, p.col = "blue", l.col = "red",
lwd = 2, ...)
``` |

`object` |
Result object from eigenvector ordination ( |

`k` |
Number of dimensions for which the ordination distances are displayed. |

`pch, p.col, l.col, lwd` |
Plotting character, point colour and line colour like in
default |

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

The functions offer a similar display for eigenvector
ordinations as the standard Shepard diagram (`stressplot`

)
in non-metric multidimensional scaling. The ordination distances in
given number of dimensions are plotted against observed
distances. With metric distances, the ordination distances in full
space (with all ordination axes) are equal to observed distances, and
the fit line shows this equality. In general, the fit line does not go
through the points, but the points for observed distances approach the
fit line from below. However, with non-Euclidean distances (in
`wcmdscale`

or `capscale`

) with negative
eigenvalues the ordination distances can exceed the observed distances
in real dimensions; the imaginary dimensions with negative eigenvalues
will correct these excess distances. If you have used
`capscale`

or `wcmdscale`

with argument
`add`

to avoid negative eigenvalues, the ordination distances
will exceed the observed dissimilarities.

In partial ordination (`cca`

, `rda`

and
`capscale`

with `Condition`

in the formula), the
distances in the partial component are included both in the observed
distances and in ordination distances. With `k=0`

, the
ordination distances refer to the partial ordination.

Functions draw a graph and return invisibly the ordination distances or the ordination distances.

Jari Oksanen.

`stressplot`

and `stressplot.monoMDS`

for
standard Shepard diagrams.

1 2 3 4 5 | ```
data(dune, dune.env)
mod <- rda(dune)
stressplot(mod)
mod <- rda(dune ~ Management, dune.env)
stressplot(mod, k=3)
``` |

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