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 Jason P. Sexton Graduate Group in Ecology University of California, Davis (530) 752-1701 jpsexton at ucdavis.edu
Mantel test!
2 messages · Jason Sexton, Sarah Goslee
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.jp at 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