I'm not Gavin, but since you posted this to the R-help list I assume you are open to other respondents.
Since you are asking Gavin, I assume you are using mantel() from the vegan package (it's a good idea to specify, as there are other possibilities). The help for that function explains the permutation test briefly, and gives a citation for more information. As for why you are getting p=1, I'd look into what hypothesis you are actually testing - quite possibly the null hypothesis that r <= 0. The mantel() function in the ecodist package offers three different hypothesis tests: r <= 0 r >= 0 r == 0 Sarah On Tue, Mar 3, 2009 at 11:24 AM, Jason Sexton <sexton...@gmail.com> wrote: > Dear Gavin, > > What is the interpretation of a simulated p-value of 1 in a mantel test and > how is the p-value derived? When we run two highly negatively correlated > matrices we get this result: r: -1, simulated p value: 1 > > I would expect the high p-value of 1 to mean not significant. Could you > clarify? > > Thank you, > > Jason > > -- Sarah Goslee http://www.functionaldiversity.org ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
