[R] cca constraining variables table

[Gavin Simpson]

On Fri, 2008-09-26 at 06:11 -0700, glaporta wrote:
> I performed canonical correspondence analysis (cca) with the example data of
> vegan, but I'm not able to obtain a table like scores() for the constraining
> variables. I can see them in the summary() mode, but it would be great to
> have in a separate table. Any suggestion?, thanx Gianandrea
> 
> require(vegan)
> data(varespec)
> data(varechem)
> vare.cca<-cca(varespec,varechem)
> scores(vare.cca)
> summary(vare.cca)
> 

You need to change from the default for scores and ask for the biplot
scores. You do this with:

scores(vare.cca, display = "bp")

to select just the biplot scores for the environmental variables.

The various types of scores and how to access them *are* documented on
the help page for ?scores.cca

All the best,

G 

-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 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
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%