Hi Callie,

Sounds to me like the permutation test is actually finding a p-value of 0,
but adds 1/10000 to make it non-zero, which is standard practice. What
values do you get when you run a different number of permutations?

-Blake

Blake Dickson
PhD Candidate
Museum of Comparative Zoology
Harvard University
26 Oxford Street
Cambridge, MA 02138

On 16 January 2018 at 13:51, Callie Diduck <diduck....@gmail.com> wrote:

>
> Hi,
>
> I am wondering if any one can help me. I have been running a Procrustes
> Rotation of Two Configurations and PROTEST using the vegan package in R.
> The Procrustes seem to be working but I am having an issue with the
> results of the PROTEST and the correlation values.
>
> I am getting identical p values every time I run the script. I have a
> sample size of 20 projectile points and every time I run the statistics my
> p value is
> equal to 0.00009999. I ran a test and I compared a circle to one of my
> projectile points and I still got a p value of 0.00009999.
>
> Here are the results for the test of the projectile point compared to a
> circle:
>
>
> Procrustes sum of squares:
>
> 1.817e+04
>
> Call:
>
> protest(X = p730, Y = pTest, permutations = 10000)
>
> Procrustes Sum of Squares (m12 squared):        0.06296
>
> Correlation in a symmetric Procrustes rotation: 0.968
>
> Significance:  9.999e-05
>
> Permutation: free
>
> Number of permutations: 10000
>
> If anyone has any idea of why this could be happening or how to fix it
> that would be greatly appreciated.
>
> Thanks
>
> Callie Diduck
>
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