Question: mantel test in vegan r package
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gravatar for haneenih7
13 months ago by
haneenih770
KAUST
haneenih770 wrote:

Hi all,

I am doing mantel test to look for the correlation between two matrices; genetic matrix and climatic distance matrix using mantel function in vegan r package This my command worked very nice

    mantel(x.dist, euc.dist.clim,  permutations = 999 , method= "pearson")

But, it's only showing the Upper quantiles of permutations, I am interested to look for the Lower quantiles of permutations as well, is there is a way to do that? the documentation doesn't show such a thing. it would be really great to have the lower quantiles of permutations 10% 5% 2.5% 1% I know that I can use other packages like the ecodist r package, where it shows the lower limit 2.5% and the upper 97.5% but I want to use vegan to show the 4 upper and lower values quantiles of permutations

here is an example of the output results;

Mantel statistic based on Pearson's product-moment correlation 
Call:
mantel(xdis = euc.dist.geo, ydis = euc.dist.clim, method = "pearson",      permutations = 999, strata = NULL) 
Mantel statistic r: 0.3255 
  Significance: 0.001 
Upper quantiles of permutations (null model):
90%    95%  97.5%    99% 
0.0390 0.0521 0.0621 0.0732 
Permutation: free
Number of permutations: 999

Thanks, Hanin

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