[R] Confusion metaMDS and CA

[swertie]

Thank you very much. I am just concerned because I wonder if I used the best
method. I have presence/absence data. With isoMDS I can specify
"Bray-Curtis" distance method, which is adequate, but I was not sure of the
method used by metaMDS. I think that it is Euclidian distance. Can I use it
for presence/absence data? 



Gavin Simpson wrote:
> 
> 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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>  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
>  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
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