R help - Jan 2009 - vegan metaMDS

Hi,

I'm trying to use metaMDS with a dissimilarity matrix of angles, not
Bray-Curtis, and I wanted to know if there is an in-built function to
produce a plot of stress values against dimensions, that could be used to
determine the 'true' dimension of the solution. The number of objects is
only a lowly 8 so any solution higher than 2-dimensional is not likely to be
interpretable, according to Kruskal and Wish's book, but this was
nevertheless required and will be useful as I gather more data. I don't have
much experience with multidimensional scaling, so any advice/reading sources
is/are welcome.

Thanks,

Radu

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Forschungsbereich Altsteinzeit
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Web: http://radu.iovita.googlepages.com/

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> Hi,
Hi Radu,
> 
> I'm trying to use metaMDS with a dissimilarity matrix
> of angles, not
> Bray-Curtis, and I wanted to know if there is an in-built
> function to
> produce a plot of stress values against dimensions, that
> could be used to
> determine the 'true' dimension of the solution. 
I am unaware of any formal test for determining the proper number of dimensions
in an NMDS ordination. It probably makes sense to think about your data and
interpretation of your solution. For example it can be hard to present a 4D
solution. Also, as I understand it the first dimension of a NMDS ordination with
2 dimensions will not be the same as the first dimension of an NMDS ordination
with 3 dimensions. The axes are arbitrary in this method.

One idea is to simply plot the stress by dimensions and look to see where the
stress levels off or drops to an acceptable level.

here is a rough example!

plot(c('2','3','4','5'),
	c(23.26272,16.37268,12.9641,10.50830), 
	xlab = 'dimensions', ylab = 'stress', type = 'b')

hope this helps,



Michael Denslow

I.W. Carpenter Jr. Herbarium [BOON]
Appalachian State University
Boone, North Carolina U.S.A.

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