Kruskal's MDS results
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
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