[R] canonical correspondence analysis
myotis at cix.compulink.co.uk
Sat Feb 17 12:18:00 CET 2001
In-Reply-To: <Pine.GSO.4.31.0102170733280.13118-100000 at auk.stats>
As an ecologist, this is something I am also interested in. However, as
I am more an ecologist than a statistician, I quote from the MVSP
"Canonical Correspondence Analysis(CCA; ter Braak, 1986,1987) is a
multivariate direct gradient analysis method that has become widely
used in ecology. As the name suggests, this method is derived from
correspondence analysis, but has been modified to allow environmental
data to be incorporated into the analysis. It is calculated using
reciprocal averaging form of correspondence analysis. However, at each
cycle of the averaging process, a multiple regression is performed of
the sample scores on the environmental variables. New site scores are
calculated based on this regression, and then the process is repeated ,
continuing until the scores stabilise. The result is that the axes of
the final ordination, rather than simply reflecting dimensions of the
greatest variability in the species data, are restricted to the linear
combinations of the environmental variables and the species data. In
this way these two sets of data are then directly related."
Ref 1: ter Braak, CJF (1986) Canonical correspondence analysis: A new
eigenfactor technique for multivariate direct gradient analysis.
Ref 2: ter Braak, CJF (1987) The analysis of vegetation-environment
relationships by canonical correspondence analysis. Vegetatio, 64:69-77
More general references are:
Jongman, RHG., Ter Braak, CJF., and, van Tongeren, OFR. (1995) Data
analysis in community and landscape ecology. CUP.
Kent, M. & Coker, P. (1992) Vegetation description and analysis: A
practical approach. Wiley.
As far as I am aware, only MVSP and Canoco carry out CCA.
I hope this is of some interest and it does raise the general point
that programming literate ecologists don't seem to have yet fully
embraced S-Plus or R. Having only recently found S-Plus and R myself I
had rather hoped that some of the common ecological statistical tools
such as CCA, Twinspan and Decorana, plus the miscellaneous tools
described in Krebs (1989) might have found there way into an R package.
Krebs, CJ (1989) Ecological Methodology, Harper & Row. Now as a 2nd
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