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
.
"stressplot"(object, k = 2, pch, p.col = "blue", l.col = "red", lwd = 2, ...)
stressplot
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.
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)
Run the code above in your browser using DataLab