[R-sig-eco] ANOSIM in vegan

[Gavin Simpson]

On Mon, 2010-11-15 at 10:09 -0500, Soumi Ray wrote:
> Thanks Jari, for your explanation!
> Could anyone explain me what does the axes scores ("points" in metaMDS
> results) represents. Are they similar to PCA factor loadings. What do these
> numerical values represent.

The best example I can come up with is that these are coordinates, like
map coordinates, in the ordination space, that is all. They are
certainly not "axis scores" in the sense of PCA et al implying that they
are independent, you need both (in 2D solution, all in k-D solutions)
coordinates to represent the "distances" between your samples in terms
of species composition.

The scores are the "best" mapping of the n-dimensional dissimilarity
matrix (n == number of sites or samples) in a k-dimensional space. Where
"best" means i) subject to convergence to a suitable global minimum in
the algorithm, and ii) the mapping is in regards to the /rank/ ordering
of the dissimilarities not their actual values.

HTH

G

> Thank you once again,
> 
> Soumi
> On Thu, Nov 11, 2010 at 7:23 PM, Soumi Ray <soumiray74 at gmail.com> wrote:
> 
> > Hi,
> >
> > I have a dataset consisting of species collected from the same location
> > during 2 time periods - i want to see if the community composition is
> > similar during the two time periods. My entire dataset is presence/absence
> > (0/1) data. There are around 23 species and 400 samples (during each time
> > period, so a total of 800 samples). Will ANOSIM from the vegan package be an
> > right test to apply? I was going through some papers online where they have
> > used methods like db-RDA in similar situations. Would it be right to use it
> > for qualitative data? Any suggestion would be of great help.
> >
> > Thanks,
> >
> > Soumi
> >
> 
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