[R] Kruskal's MDS results

[Michael Denslow]

Hi Dieter,

> I understand that the stress is a measure of how good the
> algorithm managed to represent the ordinal distances between
> items. And I also see why it's dependent on the number of
> dimensions. 
> I was hoping someone could tell me exactly what the formula
> for the percentual stress is. To me it's not clear how this
> metric is calculated.

If you have a copy of:
Venables, W. N. and Ripley, B. D. (2002) Modern Applied Statistics with S. Fourth edition. Springer. 
There is a brief section on the stress calculation. Also, I believe that the methods was first outlined in Kruskal 1963.
http://www.springerlink.com/content/010q1x323915712x/

The you can see 
MASS::isoMDS
or
MASS::Shepard
to get the exact R calculations.

Hope I helped this time,
Michael

> 
> Regards,
> Dieter
> 
> 
> Michael Denslow wrote:
> > Hi Dieter,
> > 
> > I'll take a shot at this. As I understand it, the
> stress is telling
> > you how the ordination distances compare with
> original
> > dissimilarities that you calculated.
> > 
> > It is a measure how well your ordination has done in
> representing the
> > relationship of your sites. Note that the stress will
> differ
> > depending on how many dimensions are used. I believe
> the default is k
> > = 2 in isoMDS.
> > 
> > Hope this helps, Michael
> > 
> > 
> >> Dear List,
> >> 
> >> I'm trying to interpret the results of the
> Kruskal's Non-metric
> >> Multidimensional Scaling algorithm (isoMDS, MASS
> package).
> >> 
> >> The 'goodness of fit' is reported as "The final
> stress achieved (in
> >> percent)".
> >> 
> >> What does this mean exactly? I've tried to google
> for an answer but
> >> I've not come up with a definitive answer.
> >> 
> >> Regards, Dieter
> >> 
> >> 
> >> -- Dieter Vanderelst PhD Student
> >> 
> >> Active Perception Lab University of Antwerp http://batbits.webnode.com/
> >> 
> >> Postal Address: Prinsstraat 13 B-2000 Antwerp
> Belgium
> > 
> > Michael Denslow
> > 
> > Graduate Student I.W. Carpenter Jr. Herbarium [BOON]
> Department of
> > Biology Appalachian State University Boone, North
> Carolina U.S.A.
> > 
> > -- AND --
> > 
> > Communications Manager Southeast Regional Network of
> Expertise and
> > Collections sernec.org
> > 
> > 
> > 
> 
>