Thanks a lot Gavin, that makes sense. (Sorry, clean forgot to copy the list
last time!).

Kind regards
Karen

On Mon, Nov 29, 2010 at 10:56 AM, Gavin Simpson <gavin.simpson@ucl.ac.uk>wrote:

> On Mon, 2010-11-29 at 10:38 +0200, Karen Kotschy wrote:
> > Hi Gavin
> >
> > On Mon, Nov 29, 2010 at 10:22 AM, Gavin Simpson <gavin.simpson@ucl.ac.uk
> >wrote:
> <snip/>
> > >
> > > 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.
> > >
> > >
> > You are right, the rows all contain different measures and so are not
> > strictly
> >  comparable. But they are all relative measures (proportion of the total
> > across
> >  all species, all between 0 and 1).
> >
> > Are you saying that the meaning of the "site" locations is dubious, or
> that
> > of
> > the "species" (only the latter calculated using wascores as far as I
> > understand)?
> > Should I not be using MDS for this?
>
> [Please keep replies on-list so others can contribute to the discussion]
>
> I was responding to your Q about the species WA scores. If they are all
> relative and standardised to be in the same range, then this doesn't
> seem to be too much of a problem.
>
> The sites thing is a different Q; as long as the dissimilarity you use
> is appropriate for this sort of data you should be fine.
>
> The species in your plot are located at the weighted average of the
> "sites", with the weights being the taken as "abundances" of your
> "species". For "abundances" you have relative measures on different
> diversity metrics, and "sites" are the metrics themselves. My point was,
> if you can consider the weights as being comparable, how can you compute
> a weighted average? It looks like you can make a comparison in your case
> though.
>
> I'm not too familiar with these trait-based ordinations, but taking WA
> of proportional data is fine - palaeoecologists do it every day
> reconstructing heaven-knows what from biological community data.
>
> As for interpretation; "species" points on the nMDS diagram will be
> located closer to diversity "traits" that they are relatively more
> "associated" with.
>
> HTH
>
> G
>
> > Thanks
> > Karen
> --
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