[R] any DCCA function in R?
Javier Murillo Pérez
javier.murillo at vi.ieo.es
Tue Dec 20 10:47:06 CET 2011
Thank you very much for your fast answer and your explanations.
Yes, you are right; it is in the Vegan package and I would like to run a DCCA to remove the arch effect that I obtain in a CCA. I am working with samples stations where I have my species identified and environmental variables and the idea is to do an ordination related to the environmental variables to study the assemblages that I have.
I have thought in others methods too, but I am very interesting in the CCA and it is difficult to reduce so much the number of terms, because I only have 6 environmental variables (only 6) and the most important (depth) is the responsible of this arch effect.
I have heard that CANOCO has implemented the DCCA, but as I have began to work with R some months ago and I am trying to run all my analysis with R I was interested in to know if there was any function to do this.
Could be a good idea to post that message on the R-SIG-Ecology list too.
Again thank you very much,
De: Gavin Simpson [mailto:gavin.simpson at ucl.ac.uk]
Enviado el: martes, 20 de diciembre de 2011 9:58
Para: Juan José Santos Blanco
CC: r-help at r-project.org; Javier Murillo Pérez
Asunto: Re: [R] any DCCA function in R?
On Tue, 2011-12-20 at 09:31 +0100, Juan Santos wrote:
> Dear members,
> I am performing multivariate analysis on marine benthic populations
> using R. At first glance I found ca and VEGANO packages to be the
That would be the `vegan` package
> suitable for the task, but neither has incorporated Detrended Canonical
> Correspondence Analysis (DCCA), which is just the method I want to apply
> on my data. I've looked for alternative packages containing the method,
> but my suspicion is that there is not DCCA availability for R users.
> Does anyone have better news for me?
Nope, sorry. I'm not aware of any such function and as I maintain the
Environmetric Task View on CRAN I come across most ecologically-related
packages one way or another.
I can think of two reasons to use a DCCA; i) to estimate a gradient
length in environmental space on axis 1, and ii) to remove an arch in a
ii) can more easily be addressed by reducing the number of terms in the
CCA model or a different ordination method, and i) could no doubt be
done in a number of other ways should you really want it.
As far as I am aware DCCA was only ever implemented in CANOCO (possibly
also in one of the other DOS applications from the good old days of
quantitative ecology). Jari ported the original DECORANA code for DCA to
vegan as it was available for us to do so. I am not aware of a
free/unencumbered source code for DCCA, and given that and the limited
number of applications for the method, it hasn't been something we have
been motivated to do.
What do you want to do with DCCA? Perhaps people on the list can suggest
alternatives? You might also consider posting that message (what you
want to do with DCCA) on the R-SIG-Ecology list as there'll be more
people there who will be familiar with you specific area of interest.
> Javier Murillo
> PHD Candidate
> IEO-CO VIGO
> R-help at r-project.org mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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