[R] Difference between prcomp and cmdscale

[Sarah Goslee]

On 6/14/07, michael watson (IAH-C) <michael.watson at bbsrc.ac.uk> wrote:

> ... I failed to find articles that compare and contrast PCA
> and MDS.  If you know of any, of course I would be happy to read them.

There's an excellent non-R discussion of a wide range of ordination methods
at http://ordination.okstate.edu/ (Mike Palmer's work).

If you look under "distance-based ordination" (like MDS/PCO),
you find:
"Special case: for Euclidean distance, PCoA = PCA."

and much other useful information. He also gives an extensive list of
references from the literature, if you'd like something more rigorous.
For an overview text, I'm partial to _Numerical Ecology_ by Legendre
and Legendre (1998) because of its readability, but there are many
more good texts.

Sarah
-- 
Sarah Goslee
http://www.functionaldiversity.org