[R-sig-eco] Wascores and their interpretation in metaMDS plots

[Gavin Simpson]

On Mon, 2010-11-29 at 09:37 +0200, Karen Kotschy wrote:
> Hi
> 
> I am using metaMDS in vegan to represent the dissimilarities between
> different aspects of diversity associated with a set of species (abundance,
> cover, frequency, importance value, contribution to functional diversity etc
> - each a single number per species). The diversity measures are in rows and
> the species in columns.
> 
> I get the plotting of the diversity measures ("sites" in the usual
> terminology) on the plot. What I am battling to understand is, what does
> plotting the species mean in this case? What are the wascores actually, if
> the data in the table are not abundances but other values?
> 
> What, if anything, can one read into the shape of the cloud of "species"
> (cols) points on an MDS plot of "sites" (rows)? I am getting interesting
> shapes for the cloud of "species" points and I'm just not sure how to
> interpret this.
> 
> I'd really appreciate some help. Somehow these multivariate methods always
> end up making me feel thick!!

I think the answer to this is quite simple: are the numbers for each row
("trait") comparable as a set of weights?

In a normal species matrix, the data in each cell will be count or
percentage abundance or some such similar thing. In one sense,
therefore, we can say that the data are all in the same units. This
isn't the case from your description of the data, above.

If they are not comparable (or standardised/normalised to make them
comparable), and I don't see how they can be/are, I would struggle to
conceptualise what a weighted mean of site locations on the nMDS plot
would mean if the weights were such disparate types of data.

G

> Thanks
> Karen
> 
> ---
> Karen Kotschy
> Centre for Water in the Environment
> University of the Witwatersrand, Johannesburg, South Africa
> 
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