sammon(d, y=cmdscale(d), k=2, niter=100, trace=T, magic=0.2, tol=1e-4)
d
|
distance structure of the form returned by dist , or a full, symmetric
matrix. Data are assumed to be dissimilarities or relative distances,
but must be positive except for self-distance.
|
y
|
An initial configuration. If none is supplied, cmdscale is used to provide
the classical solution.
|
k
| The dimension of the configuration. |
niter
| The maximum number of iterations. |
trace
|
Logical for tracing optimization. Default True .
|
magic
| initial value of the step size constant in diagonal Newton method. |
tol
| Tolerance for stopping, in units of stress. |
An iterative algorithm is used, which will usually converge in around
50 iterations. As this is necessarily an O(n^2) calculation, it is slow
for large datasets. Further, since the configuration is only determined
up to rotations and reflections (by convention the centroid is at the
origin), the result can vary considerably from machine to machine.
In this release the algorithm has been modified by adding a step-length
search (magic
) to ensure that it always goes downhill.
points
| A two-column vector of the fitted configuration. |
stress
| The final stress achieved. |
cmdscale
, isoMDS
data(swiss) swiss.x <- as.matrix(swiss[, -1]) swiss.sam <- sammon(dist(swiss.x)) plot(swiss.sam$points, type="n") text(swiss.sam$points, labels=as.character(1:nrow(swiss.x)))