Lauren, I am not aware of a single publication that uses 'goodness statistics' to remove species from ordination plots. But that does not mean it is not common practice (just as failure to report nonsignificant results may be common practice...).
On another point, removing species from display (often a practical necessity) is very different from removing a species from analysis (which, if the idea is to understand species composition, is often a shady proposition if not justifiable on a priori grounds). I hope most authors will provide criteria for removing species from display, and if not, reviewers should be on guard. --Mike Michael W. Palmer, Regents Professor, Botany Department, Oklahoma State University 104 LSE Stillwater OK 74078 USA 405-744-7717 LABORATORY FOR INNOVATIVE BIODIVERSITY RESEARCH AND ANALYSIS: http://ecology.okstate.edu/Libra/ Wildfuels Blog: http://cas.okstate.edu/debo/blogs/ OSU Botany: http://botany.okstate.edu/ OSU Ecology: http://ecology.okstate.edu -----Original Message----- From: Ecological Society of America: grants, jobs, news [mailto:[email protected]] On Behalf Of L Quinn Sent: Monday, November 23, 2009 1:49 PM To: [email protected] Subject: [ECOLOG-L] vegan package: goodness.cca function Hello, I am posting this to R-help and Ecolog-L, in hopes that enough Ecologgers are R users and enough R-help users are ecologists. Please forgive the cross-posting. I deleted a number of species from a canonical correspondence analysis (CCA) model after using the function goodness.cca in vegan. In his explanation of the diagnostic tools for CCA (http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/goodness.cca.html), Jari Oksanen states that "It is a common practise to use goodness statistics to remove species from ordination plots". However, I have not been able to find references on this "common practice" in the literature. I may be using inappropriate search terms?? However, if anybody can point me towards some cite-able references/rules of thumb on this, I would very much appreciate it. And yes, I am also aware that Jari goes on to say that deleting species isn't always a good idea. Thank you! Lauren Quinn _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/
