[R-sig-eco] repeated measures NMDS?

Eduard Szöcs szoe8822 at uni-landau.de
Wed Nov 10 13:57:25 CET 2010

Thanks, that helped.

permuted.index2() generates these types of permutations. But envfit() 
does not use this yet.
What if I modify vectorfit() (used by envfit() ) in such a way that it 
uses permuted.index2() instead of permuted.index()?

Eduard Szöcs

Am 08.11.2010 22:01, schrieb 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.
> G

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