[R] Mantel test!

[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