[R-sig-eco] using two distance metrices in formula

[Gavin Simpson]

On Wed, 2009-10-14 at 09:13 +0200, Maarten de Groot wrote:
> Dear Jens,
> 
> As far as I understood you are looking for the influence of one distance 
> matrix on another. (Please correct me if I am wrong) Than the following 
> reference might be useful:
> 
> ter Braak, C. J. F. and Schaffers, A. P. 2004: Co-correspondence 
> analysis: a new ordination method to relate two community compositions. 
> Ecology 85, 834-846.
> 
> I don't know whether this is implemented in R, though.

It is, in the cocorresp package (by yours truly); although I think it
fair to say that whilst the package will do the necessary computations,
the associated functions for plotting ordination results and the like
are somewhat lacking, very much so when compared to the offerings in
packages like vegan and ade4. The code does little more than the Matlab
code provided with the paper you cite.

>From my reading of the thread and Jens' postings, Co-CA probably isn't
quite the right method as it was specifically designed for two species
matrices and uses an underlying unimodal response model like CA; you
could think of Co-CA as a version of CCA that allows unlimited
constraints and fits a non-linear (instead of linear) model in those
constraints.

Furthermore, Co-CA, and its implementation in cocorresp, requires the
original data matrices on both sides of the model formula, not
dissimilarity matrices.

HTH

G

> 
> Kind regards,
> 
> Maarten
> 
> Sarah Goslee wrote:
> > That doesn't make much sense to me. You'd need an entirely different method
> > than capscale.
> >
> > Perhaps what you're looking for is more like multiple regression on distance
> > matrices (implemented in MRM in ecodist)?
> >
> >      Lichstein, J. 2007. Multiple regression on distance matrices: A
> >      multivariate spatial analysis tool. Plant Ecology 188: 117-131.
> >
> >      Legendre, P.; Lapointe, F. and Casgrain, P. 1994. Modeling brain
> >      evolution from behavior: A permutational regression approach.
> >      Evolution 48: 1487-1499.
> >
> > Sarah
> >
> > On Tue, Oct 13, 2009 at 11:13 AM, Jens Oldeland <oldeland at gmx.de> wrote:
> >   
> >> Dear Sarah dear Jari,
> >>
> >> many thanks for your explanations. However, it wasnt what I thought about,
> >> sorry I definitely have to be more specific about the problem.
> >>
> >> Okay I try be more precise:
> >>
> >> the problem was that for example  capscale accepts   "capscale(dist.matrix.1
> >> ~ N + P + K *Ag, data=varechem)"
> >> but I need  "capscale(dist.matrix.1 ~ dist.matrix.2, data=dist.matrix.2)"
> >>  so the trick was not on how to create a distance matrix but how to use a
> >> second on in a formula.
> >>
> >> We are trying a similar analysis like the the "distlm" program by Marti
> >> Anderson does, however we had a problem with that and wanted to try the
> >> analysis in R.
> >>
> >> thanks already for all your comments !
> >>
> >> best
> >> Jens
> >>     
> >
> >
> >
> >
> 
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