[R-sig-eco] ANOSIM in vegan

[Gavin Simpson]

On Wed, 2010-11-24 at 10:21 +0100, Michael Gerisch wrote:
> Hi Soumi,
> 
> it just came into my mind - no idea if i am wrong: For me it sounds like your 
> sampling design is not independent, as you sample 400 plots twice and you will 
> have high probability that the community of a pair of similar sites is more 
> equal just because it is the same site and not because of some environmental 
> factors. Call it pseudoreplication or else, but i think large part of the 
> "similarity" will be due to this fact. Unless you have something like an 
> extreme event between the dates which sort of "reset" your communites...maybe 
> then its appropriate.
> 
> But i don`t know if anosim has the assumption of independence anyway. Maybe 
> there is "reanypeated measure" variant? Or maybe i am  totally wrong...

I don't think ANOSIM has many assumptions at all - we test using
permutations and so long as you can generate an appropriate Null
distribution that respects the dependence structures in the data, we can
provide a test. Generating the appropriate Null requires doing a lot by
hand at the moment if you want anything but random permutations (or
random within blocks).

Think of Soumi's Q the other way round. We want to test if there is a
difference in community composition in sample between times A and B. The
TIME variable would explain all the temporal dependence structure. If
there is no other dependence structure (say spatial, or spatially
correlated environmental dependence - the effect of an env var across
the survey sites), then we could assume a Null distribution for the
permutation via random permutation - the residuals are assumed random in
that case.

The issue to hand (in your email) is dependence in the residuals - in
general in statistical methods. If you model this dependence such that
the residuals meet the assumptions of the method, you are fine. It is
only an issue when you fail to (or can't) model the dependence structure
as part of the statistical method itself. Because then the residuals
will not be independent, identically distributed etc.

HTH

G

> Sorry, did not want to confuse, but it would also be interesting for me.
> 
> cheers
> michael
> 
>   
> 
> On Friday 12 November 2010 01:23:41 Soumi Ray wrote:
> > Hi,
> > 
> > I have a dataset consisting of species collected from the same location
> > during 2 time periods - i want to see if the community composition is
> > similar during the two time periods. My entire dataset is presence/absence
> > (0/1) data. There are around 23 species and 400 samples (during each time
> > period, so a total of 800 samples). Will ANOSIM from the vegan package be
> > an right test to apply? I was going through some papers online where they
> > have used methods like db-RDA in similar situations. Would it be right to
> > use it for qualitative data? Any suggestion would be of great help.
> > 
> > Thanks,
> > 
> > Soumi
> > 
> > 	[[alternative HTML version deleted]]
> > 
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> 

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