On 8 Dec 2008, at 2:53, stephen sefick wrote:
A way that may work is use the axis scores as y in a regression- this
seems like it would let you interpret how the communities are
distributed in species space. Just a thought
NEVER do this! The rotation is not determined in NMDS. If you rotate
the NMDS solution you will always have the very same solutios, but the
correlations with the "axis scores" will change. The whole point of
having envfit/vectorfit in vegan is that you don't need to calculate
the correlations with the axes.
The axis rotation is determined in eigenvector ordination, but that
does not mean that the direction is meaningful. You can see this with
envfit/vectorfit in unconstrained eigenvector ordination, but also in
constrained ordination: very rarely the fitted vectors or biplot
arrows are parallel to axes. Only if axes are parallel to axes (and go
along the axes), then it would be meaningful to look a the
relationship of axis and something else.
And indeed, there is no constrained NMDS in vegan. It is unconstrained
with an interpretation through vector fitting.
cheers, jari oksanen
Stephen Sefick
On Sat, Dec 6, 2008 at 11:58 AM, Manuel Spínola
<[EMAIL PROTECTED]> wrote:
Dear list members,
Is there any reference or document on how to interpret a
"constrained"
non-metrical multidimensional scaling using ecological data? By
"constrained" I mean after fitting environmental covariables,
using, for
example, the "envfit" function in the vegan package. Is it
possible to
interpret the resulting plot in the same way that a constrained
ordination,
for example CCA?
Thank you very much in advance.
Best,
Manuel
--
Manuel Spínola, Ph.D.
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
[EMAIL PROTECTED]
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Fax: (506) 2237-7036
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Stephen Sefick
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
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