[R-sig-eco] repeated measures NMDS?

[Gavin Simpson]

On Mon, 2010-11-08 at 15:39 +0100, Eduard Szöcs wrote:
> Hi listers,
> 
> I have species and environmental data for 24 sites that were sampled
> thrice. If I want to analyze the data with NMDS I could run metaMDS on
> the whole dataset (24 sites x 3 times = 72) and then fit environmental
> data, but this would be some kind of pseudoreplication given that the
> samplings are not independent and the gradients may be overestimated,
> wouldn`t it?
> 
> For environmental data a factor could be included for the sampling
> dates - but this would not be possible for species data.
> 
> Is there an elegant way either to aggregate data before ordination or
> to conduct sth. like a repeated measures NMDS?
> 
> Thank you in advance,
> Eduard Szöcs

Depends on how you want to fit the env data - the pseudo-replication
isn't relevant o the nMDS. If you are doing it via function `envfit()`,
then look at argument `'strata'` which should, in your case, be set to a
factor with 24 levels. This won't be perfect because your data are a
timeseries and, strictly, one should permute them whilst maintaining
their ordering in time, but as yet we don't have these types of
permutations hooked into vegan.

If you are doing the fitting some other way you'll need to include
"site" as a fixed effect factor to account for the within site
correlation.

You don't need to worry about the species data and accounting for
sampling interval. You aren't testing the nMDS "axes" or anything like
that, and all the species info has been reduced to dissimilarities and
thence to a set of nMDS coordinates. You need to account for the pseudo
rep at the environmental modelling level, not the species level.

HTH

G

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