[R] cca with repeated measures

René Mayer mayer at psychologie.tu-dresden.de
Fri Nov 18 15:17:39 CET 2011

Thanks a lot Gavin!,
this was what I was looking for.
Have I got this right that with no 'cyclic shifts *within* strata' you  
mean that I cannot define a nesting within animal, e.g.,  
animal/year/season (speaking in regression-terms  random-effects for  
the animal-specific season and year variation).

Dr. René Mayer                   Email: mayer at psychologie.tu-dresden.de
Research Assistant               Phone: +49-351-463-34568
Department of Psychology         Fax:   +49-351-463-33522
Dresden University of Technology Web:   http://tu-dresden.de/en

Zitat von "Gavin Simpson" <gavin.simpson at ucl.ac.uk>:

> On Fri, 2011-11-18 at 10:25 +0100, René Mayer wrote:
>> Dear all,
>> How can I run a constrained correspondence analysis with
>> the following data:
>> 15 animals were measured repeatedly month-wise (over to 2 years)
>> according to ther diet composition (8 food categories).
>> our data.frame looks like this:
>> food 1  2 ... 8  sex season year animal
>> freq 12 8 ... 1  0   summer 2011 1
>> freq 0  7 ... 0  1   winter 2011 1
>> ...
>> freq 0  7 ... 0  1   spring 2011 15
>> We want to find out if season and sex influences diet composition.
>> My experience with CCA is limited, but in repeated measures ANOVA,
>> e.g. with aov()
>> on has to define the between (animal) error term in order to deal with
>> the pseudoreplication.
>> Do I have to restructure or reshape the data in order to deal with
>> pseudoreplication
>> the data? Or do I have to define an error strata?
>> I suspect I cannot simply run:
>> library(vegan)
>> model=cca(food ~ season*sex+year+animal, data)
> You could do that although the analysis would be i) focussed on those
> particular animals in those years, and ii) you could only test the terms
> season, sex and season:sex in a sequential manner (i.e. dependent upon
> how the terms enter the model), so season, then sex after season is in
> the model, then their interaction after both main terms are included in
> the model.
> ii) is done by adding `by = "terms"` to the call to the `anova method
> for "cca" objects; examples are in `?anova.cca`
> That corresponds to a fixed effects formulation of the ANOVA (assuming I
> have my terminology right). The alternative is to adjust the permutation
> scheme used to reflect the clustering in your data. In that case, using
> `strata = animal` would be OK. Ideally one would want to control for
> temporal dependence so you would want cyclic shifts *within* `strata =
> animal` but vegan can not yet do this sort of permutation. It is coming;
> the actual code to generate those permutations is available in the
> permute package (upon which vegan depends), but as yet we have not
> hooked this into the vegan ordination functions (it is on the TODO
> list). That said, season should be accounting for much of the temporal
> dependence, so I think you might get away with just specifying strata
> (the permutation test itself is permuting residuals from the model so if
> the model is capturing the seasonal variation then the simple permuting
> within animal should be OK, but you can check by extracting the
> residuals using the resid() method and plotting them out by time and
> animal).
> G
>> I would be grateful for any help.
>> Thanks in advance,
>> René
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