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 > > > > > > > > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
