[R-sig-eco] procrustes() and protest() in vegan: any hints on the interpretation?

[Gian Maria Niccolò Benucci]

Good morning r-sig-ecologists,
I have a question for you on how to have a correct interpretation of
protest() output. I have read the R documentation where it is reported that
a correlation-like statistics is computed from the symmetric Procrustes sum
of squares also called squared m12 = sqrt(1-ss). Based on my knowledge, the
smaller the residual sum of squares, the better your model fits your data.
In this context my question is: Do I need a "big" m12 to say that my two
ordination configuration were matching?
Below my protest() result:

>protest(X = fungi_NMDS_LSU, Y = fungi_NMDS_ITS, permutations = 999)

Procrustes Sum of Squares (m12 squared):        0.111
Correlation in a symmetric Procrustes rotation: 0.9429
Significance:  0.001

Permutation: free
Number of permutations: 999

Thank you for your help,

-- 
Gian

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