On Mon, 14 Apr 2003, St?phane Deraco wrote:
> I try to calculate the stress of a configuration using the formula in
> the isoMDS help,
You used a very different formula than the description on that page (which
does not contain a formula).
> but I don't have the same result than the stress
> returned by isoMDS :
>
> > library(mva)
> > library(MASS)
> > data(swiss)
> > swiss.x <- as.matrix(swiss[,-1])
> > swiss.dist <- dist(swiss.x)
> > swiss.mds <- isoMDS(swiss.dist)
> initial value 2.979731
> iter 5 value 2.431486
> iter 10 value 2.343353
> final value 2.338839
> Converged
> >
> > delta.x <- swiss.mds$points
> > delta.dist <- dist(delta.x)
> >
> > stress <- function(avant, apres) {
> + l <- length(avant)
> + num <- 0
> + denum <- 0
> +
> + for (i in 1:l) {
> + num <- num + (avant[i] - apres[i])^2
> + denum <- denum + apres[i]
> + }
> +
> + sqrt(num / denum)
> + }
> >
> > swiss.mds$stress
> [1] 2.338839
The help page says that is a *percentage*.
> > stress(swiss.dist, delta.dist)
> [1] 0.4196349
> >
>
>
> Any idea ?
Use the right formula:
However, the input distances are allowed a monotonic
transformation.
and you haven't allowed one. You have also forgotten to multiply by 100.
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595