[R] Mantel test!

Sarah Goslee sarah.goslee at gmail.com
Tue Mar 3 17:51:24 CET 2009

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


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

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