[R] Plot of Canonical Correlation Analysis

Gavin Simpson gavin.simpson at ucl.ac.uk
Fri Mar 28 12:52:02 CET 2003

If the original poster actually meant output from cancor() in library(mva)
then I don't think Jari's vegan package will necessarily work "out of the
box" for objects created using cancor().

Quoting the help file on scores() :
Currently the function seems to work at least for `isoMDS', `prcomp',
`princomp', `ca', `pca'.  It may work for other cases, or fail mysteriously.

I've just looked at the code for scores() in vegan (which is used to plot
non-vegan-created ordination results) and it does not know about the values
returned in a cancor object (cor, xcoef, ycoef, xcenter, ycenter etc.).

There has been confusion over the use of three letter acronyms for methods
in community ecology with some people using CCA for canonical correlation
analysis, and others, like Jari and in the limnology/ecology field, using
CCA to mean Canonical Correspondence Analysis.  The two methods are very
different.  (I prefer CCA = Canonical Correspondence Analysis myself - but
that how I learned the method!)

Hope this helps.


Gavin Simpson                     [T] +44 (0)20 7679 5522
ENSIS Research Fellow             [F] +44 (0)20 7679 7565
ENSIS Ltd. & ECRC                 [E] gavin.simpson at ucl.ac.uk
UCL Department of Geography       [W] http://www.ucl.ac.uk/~ucfagls/cv/
26 Bedford Way                    [W] http://www.ucl.ac.uk/~ucfagls/
London.  WC1H 0AP.

-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Anon.
Sent: 28 March 2003 11:29
To: f.mercier at fournier.fr
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Plot of Canonical Correlation Analysis

f.mercier at fournier.fr wrote:
> Dear all,
> I didn't find any graphical solution in the package "mva" to plot the
> canonical scores from a CCA (canonical correlation analysis).
> Does anybody knows how to plot or has anybody already programmed :
>       - the map of the canonical scores,
>       - the graph of the canonical weights,
>       - the correlation circle i.e. the canonical loadings ?
> Thank you for help ...
Have a look at Jari Oksanen's vegan package.  It's on CRAN, but it also 
has its own page: <http://cc.oulu.fi/~jarioksa/softhelp/vegan.html>


Bob O'Hara

Rolf Nevanlinna Institute
P.O. Box 4 (Yliopistonkatu 5)
FIN-00014 University of Helsinki
Telephone: +358-9-191 23743
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Fax:  +358-9-191 22 779
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