isoMDS {MASS}  R Documentation 
One form of nonmetric multidimensional scaling
isoMDS(d, y = cmdscale(d, k), k = 2, maxit = 50, trace = TRUE, tol = 1e3, p = 2) Shepard(d, x, p = 2)
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 selfdistance. Both
missing and infinite values are allowed.

y 
An initial configuration. If none is supplied, cmdscale is used
to provide the classical solution, unless there are missing or
infinite dissimilarities.

k 
The desired dimension for the solution, passed to cmdscale .

maxit 
The maximum number of iterations. 
trace 
Logical for tracing optimization. Default TRUE .

tol 
convergence tolerance. 
p 
Power for Minkowski distance in the configuration space. 
x 
A final configuration. 
This chooses a kdimensional (default k = 2) configuration to minimize the stress, the square root of the ratio of the sum of squared differences between the input distances and those of the configuration to the sum of configuration distances squared. However, the input distances are allowed a monotonic transformation.
An iterative algorithm is used, which will usually converge in around 10 iterations. As this is necessarily an O(n^2) calculation, it is slow for large datasets. Further, since for the default p = 2 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.
Two components:
points 
A kcolumn vector of the fitted configuration. 
stress 
The final stress achieved (in percent). 
If trace
is true, the initial stress and the current stress
are printed out every 5 iterations.
T. F. Cox and M. A. A. Cox (1994, 2001) Multidimensional Scaling. Chapman & Hall.
Ripley, B. D. (1996) Pattern Recognition and Neural Networks. Cambridge University Press.
Venables, W. N. and Ripley, B. D. (2002) Modern Applied Statistics with S. Fourth edition. Springer.
data(swiss) swiss.x < as.matrix(swiss[, 1]) swiss.dist < dist(swiss.x) swiss.mds < isoMDS(swiss.dist) plot(swiss.mds$points, type = "n") text(swiss.mds$points, labels = as.character(1:nrow(swiss.x))) swiss.sh < Shepard(swiss.dist, swiss.mds$points) plot(swiss.sh, pch = ".") lines(swiss.sh$x, swiss.sh$yf, type = "S")