[R-sig-eco] advice on joining replicates

[Gavin Simpson]

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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