hello, subsequently to a NMDS analysis (performed with metaMDS or isoMDS) is it possible to rotate the axis through a varimax-rotation? Thanks in advance. Bernd Panassiti
NMDS and varimax rotation
6 messages · Bernd Panassiti, stephen sefick, William Revelle +1 more
have you looked at the vegan viginette- I know there is proscrutes rotation. On Tue, Sep 9, 2008 at 3:54 PM, Bernd Panassiti
<bernd.panassiti at uni-rostock.de> wrote:
hello, subsequently to a NMDS analysis (performed with metaMDS or isoMDS) is it possible to rotate the axis through a varimax-rotation? Thanks in advance. Bernd Panassiti
______________________________________________ R-help at 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.
Stephen Sefick Research Scientist Southeastern Natural Sciences Academy Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis
At 9:54 PM +0200 9/9/08, Bernd Panassiti wrote:
hello, subsequently to a NMDS analysis (performed with metaMDS or isoMDS) is it possible to rotate the axis through a varimax-rotation? Thanks in advance. Bernd Panassiti
Bernd, Yes. The output of isoMDS is an object with points and stress. consider the following example: test.data <- Harman74.cor$cov #twenty four mental measurements harm.dist <- sqrt(2*(1- test.data) ) #convert correlations to distances harm.iso <- isoMDS(harm.dist,k=2) # find the multidimensional solution harm.varimax <- varimax(harm.iso$points) #rotate with varimax op <- par(mfrow=c(1,2)) plot(harm.iso$points, main="unrotated") plot(harm.varimax$loadings,main="rotated") Bill
______________________________________________ R-help at 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.
William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org/personality.html Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Use R for psychology http://personality-project.org/r
hello, thanks a lot for your help. @ Stephen: In my opinion the proscrutes rotation is more used to compare the alignment of different ordination methods. But maybe I'm wrong. @ Bill: Thanks for the comprehensive description. That was the information I was looking for. Greetings, Bernd Panassiti
On Wed, 2008-09-10 at 14:24 +0200, Bernd Panassiti wrote:
hello, thanks a lot for your help. @ Stephen: In my opinion the proscrutes rotation is more used to compare the alignment of different ordination methods. But maybe I'm wrong. @ Bill: Thanks for the comprehensive description. That was the information I was looking for.
Isn't Varimax rotation what is done in PCA? If so, metaMDS() does this rotation by default (via postMDS() and it's 'pc' argument). So this feature may already be implemented in the metaMDS wrapper to MASS::isoMDS that you mention. G
Greetings, Bernd Panassiti
______________________________________________ R-help at 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.
hello Gavin, yes, you might be right. I performed a comparison of a normal NMDS (with metaMDS) and a subsequent rotation with varimax. The rotation didn't seem to improve significantly the the alignment of the former ordination output. Thanks for your hint & greetings. Bernd Panassiti