Hi Gavin and others,

I do not want to throw away the data, however to best of my knowledge,
methods like CCA, nMDS, decorana, envfit require samples. I would currently
not know how to implement intact replicates into the analysis.

Cheers,
Roman



On Fri, Jan 22, 2010 at 10:12 AM, Gavin Simpson <gavin.simpson@ucl.ac.uk>wrote:

> On Thu, 2010-01-21 at 22:30 +0100, Roman Luštrik wrote:
> > Dear List,
> >
> > I realize my question may not be as R related as expected, but hopefully
> > subscribers will overlook this and hopefully offer some advice.
> > I have 10 stations with each station having 5 replicates (50 samples in
> > total). I would like to join the replicates into one sample for further
> > analysis. Unfortunately I can't find how other studies joined replicates
> > (most paper I've read only note how they grouped species). Due to lack of
> > references, I joined samples around their median. This shrunk my initial
> > dataset of 83 species to 29. If I follow the advice by Warwick and Clarke
> > (PRIMER-E manual) and remove species contributing less than 1 or 2% to
> total
> > abundance, I end up with 14 and 11 species, respectively. Is there a
> better
> > way of grouping replicates than by median?
> >
> > Cheers,
> > Roman
>
> Why do you want to throw away data? Can't you account for the clustering
> in your data within the "further analysis" you are going to undertake?
>
> Depending on your research question or how you view ecosystems etc,
> throwing away the rare taxa may not be the best idea either...
>
> Perhaps if you explain what it is that you will do in "further analysis"
> we can provide options?
>
> G
>
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