[R-sig-eco] Multivariate ANOVA/repeated measures

[Dave Roberts]

On 10/10/2011 02:15 PM, Gavin Simpson wrote:
> On Mon, 2011-10-10 at 09:11 -0700, Rich Shepard wrote:
>> On Mon, 10 Oct 2011, Dave Roberts wrote:
>>
>>>> I want to compare the results of the two sampling exercises in order to
>>>> test the performance of the two sampling techniques.
>>
>>>    I would try something pretty direct. Any appeal to differences in
>>> dissimilarities confounds the effects with the particular
>>> dissimilarity/distance matrix you use. Assuming the samples and species
>>> are in the same order, and that the data.frames are the same size, you
>>> might try
>>
>>     I did not read the original message, so I hope you'll allow me to join the
>> thread. My recommendation is to use univariate tree models, particularly a
>> classification tree (for ordinal explanatory variables; i.e., ST1 and ST2).
>
> But the response here is *multivariate* - of course, one could use Glen
> De'Ath's multivariate regression trees (despite the name it is really a
> constrained clustering/classification) - but I think there are better
> ways of solving this particular problem. And unless one has many 100s of
> observations, the model will need some sort of variance reduction
> applied (via bagging, or some such) as the one fitted model is
> potentially highly unstable.
>
> G
>
>>     This is fully, carefully, and non-technically explained in Chapter 9
>> (particularly Sections 9.3 and 9.4) in Zuur, Ieno, and Smith "Analysing
>> Ecological Data." For that matter, I highly recommend reading the whole
>> book.
>>
>> Rich
>>
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>

It would be fairly simple to boil down to a univariate question.  You 
could do something as simple as a paired t-test of plot-level species 
richness or the number of individuals sampled (to compare sampling 
efficiency), but I still don't see an independent and a dependent variable.

Dave
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