On Tue, 2008-07-22 at 15:22 -0700, joseph gathman wrote: > Dear Ecologgers, > > I'd like to hear opinions on community analysis/ordination software, > especially PC-ORD vs. Brodgar/R. I'd like to be able to run a full > array of analyses, so I don't think CANOCO will do (pretty darned > expensive, too). I understand that PC-ORD is considerably cheaper, > given the current weak dollar, but does anybody out there have > comments on versatility, ease of use, learning curve (I haven't taught > myself R yet)? > > You can send responses directly to me, if you prefer.
[Full disclosure: I'm probably very biased here as I use R for 99% of my analysis tasks, and am a contributor to several R packages for ecological data analysis] R, on its own (well with a text editor to write the scripts; Emacs + ESS is my personal preference) and the vegan package, plus various packages in the (shameless plug) Environmetrics Task View: http://cran.r-project.org/web/views/Environmetrics.html would be my choice for what you describe. A further advantage is that new analysis techniques are being written in, or are already available in (or can be easily ported to) R. Of course, R has a fairly steep learning curve. I'd advise you to try to find an introductory course near to you so you can learn to use R. Not because you can't do it on your own (I did as a PhD student 8 years ago), but because unless you have the time to set aside to go through some of the introductory materials and manuals, you're likely to find R frustrating if you jump straight in and try to do some analysis for a job that needs to be done. At least on a course, you are there to learn... One of the advantages of Canoco over competing packages (IMHO, and also based on experiences from several years ago - things may have changed in the intervening period) was the availability of comprehensive support for restricted permutations that allow complex, designed experiments to be analysed via appropriate permutations tests; random shuffling is often not suitable due to spatial/temporal autocorrelation, or blocks/split plots etc. This latter point applies to vegan as well of course, but we are getting closer to the permutation functionality available in Canoco. HTH G > > Thanks, > Joe Gathman > Asst. Prof. > U. Wisconsin - River Falls > > >
