[R-sig-eco] repeated measures NMDS?

[Gavin Simpson]

On Wed, 2010-11-10 at 13:57 +0100, Eduard Szöcs wrote:
> 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()?

permuted.index2() is old code. Don't use it. Or at least if you do,
check it works for your permutation design.

I carved off this code into a new package `permuted` which is part of
the vegan stable on R-Forge. `permute` generates the correct
permutations but needs a bit of work on the surrounding helper code.

If you want the same permutation, temporally constrained, then really
you only have 72 permutations of your data and should evaluate all of
them, not at random. `permute` is designed to generate the set of
permutations for you, but there are bugs in it that mean it doesn't work
for all designs as yet.

Sorry I can't be much more help at the moment - I'm busy with work and
about to head into the field for 10 days.

HTH

G

> 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.
> >
> > HTH
> >
> > G
> >
> 

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