[R] canonical correspondence analysis

Prof Brian Ripley ripley at stats.ox.ac.uk
Mon Feb 26 16:03:49 CET 2001

> Date: Mon, 26 Feb 2001 16:37:15 +0200
> From: Jari Oksanen <jarioksa at sun3.oulu.fi>
> * CCA which is the canonical ordination method in community ecology nowadays: 
> filling this gap would be really good (this is not my personal opinion, which 
> is more sceptical, but the general opinion). I'd glad to see the functions, if 
> they are available (and I think the eigenvector, or svd, version should be 
> favoured instead of the original power algorithm look-alike).

A package by Stephane Dray that covers CCA is in preparation and will
be on CRAN shortly.


> * Venables' & Ripley's isoMDS (and perhaps even more interestingly: sammon) 
> are already available, but they'd need some extra tools for community 
> ecologists. Most importantly, an additional package to `dist' with 
> ecologically more relevant distance measures: those that have a good 
> rank-order correlation with ecological distances with unimodal species 
> responses along ecological axes (`gradients').  By the way, the default 
> practice of using metric scaling as the starting configuration in isoMDS is 
> almost guaranteed to fall into local optima: I have tested with some data sets 
> using random starting configurations and usually managed to find much lower 
> stresses than the default (this is in common with most implementations of MDS 
> in statistical packages).

Sure, but that is a feature not a bug.  You search for a local minimum
near the starting point.  If you don't like cmdscale as a starting point
you can easily supply another.  There is no way to do other than
local minimization, and not much reason to suppose that the answer is
a particularly compelling one.

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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