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.
# S3 method for wcmdscale
stressplot(object, k = 2, pch, p.col = "blue", l.col = "red",
lwd = 2, ...)Functions draw a graph and return invisibly the ordination distances or the ordination distances.
Result object from eigenvector ordination (wcmdscale,
rda, cca, dbrda,
capscale)
Number of dimensions for which the ordination distances are displayed.
Plotting character, point colour and line colour like in
default stressplot
Other parameters to functions, e.g. graphical parameters.
Jari Oksanen.
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, dbrda 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 dbrda,
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. The exception is
dbrda where the distances in partial, constrained and
residual components are not additive, and only the first of these
components can be shown, and partial models cannot be shown at all.
stressplot and stressplot.monoMDS for
standard Shepard diagrams.
data(dune, dune.env)
mod <- rda(dune)
stressplot(mod)
mod <- rda(dune ~ Management, dune.env)
stressplot(mod, k=3)
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