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 > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
