[Taxacom] Principal Components Analaysis - help with a good reference and software

tyler tyler.smith at mail.mcgill.ca
Fri Feb 13 11:39:09 CST 2009

Mark Watson writes:

 > Could someone please recommend me a good student text (print or
 > internet site) explaining the theory and practice of Principal
 > Components Analysis as it is applied to assessing morphological
 > variation in biology?

For taxonomic application, I still like Sneath and Sokal's Numerical
Taxonomy (1973). It's fairly accessible, and while it's dated, most
recent texts are more focused on ecology.

Mike Palmer has some tutorial material, aimed at ecologists:

It's been highly recommended, but I've only skimmed it.

'Student' can mean different things, of course. If your student is a
grad student looking forward to a career in morphological taxonomy, it
will be worth working through Legendre and Legendre (1998), at least
as far as the clustering and ordination chapters.

 > I am also looking around at various software options for PCA, so
 > advice on this would also be very helpful.

Again, it depends on what kind of student you've got. If they're an
honours student with a project that needs to be completed on a tight
timeline, CANOCO is easy to use and comes with help files that are
actually quite helpful. On the other hand, for grad students, time
invested in learning R is a good investment. Jari Oksanen has some
ordination tutorials based on R at his website:




Don't learn the tricks of the trade; learn the trade.

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