[R] Confusion metaMDS and CA

[Gavin Simpson]

On Thu, 2009-09-03 at 04:49 -0700, swertie wrote:
> Hello, I read a lot about ordination, but I am still confused... I have data
> on species presence/absence for 8 different sites and I would like to
> represent my species and the sites on an ordination plot to see if some
> species are associated with specific sites. I used metaMDS function, which
> displays both sites and species and it seems to work well. However why are
> most people using CA instead of non metric multidimensional scaling? Thank
> you  

Inertia ;-)

It's what they were taught, because that's what their supervisors were
taught etc.

CA has a long history within ecological circles and most people will be
familiar with it.

nMDS is an iterative algorithm that may nor may not converge to "the"
solution. There may not be "one" solution but rather many equally good
ones. It takes a lot more effort (well, if you are outside of R) to run
nMDS properly and check you're not converging to a local solution.

There are lots of reasons. Why are interested in this; are you concerned
you've done something wrong or inappropriate with your data?

HTH

G

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