[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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