[R] RDA permutest envfit

[Rémi Lesmerises]

Dear all,

I did a RDA and when I looked to the signification of the test with permutest, 
the output was non-significant. But when I used the envfit function, some of 
the vectors are significant. All the test's conditions are respected. What it 
means? Is it an error in the script?


Commands and output:

> permutest(rda.ind, perm=999, first=TRUE)

Permutation test for rda 

Call: rda(formula = x ~ ARH_frs + CON_frs + PRP_frs + RUI_frs + VAM_frs, data = 
z)
Permutation test for first constrained eigenvalue
Pseudo-F:        4.093568 (with 1, 10 Degrees of Freedom)
Significance:    0.413 
Based on 999 permutations under reduced model.

> fit <- envfit(rda.ind, z, perm = 999, display = "lc")
> fit

***VECTORS

             RDA1      RDA2     r2 Pr(>r)    
VAM_frs  0.145281 -0.989390 0.2388  0.147    

ARH_frs -0.876494 -0.481413 0.6127  0.002 ** 
CON_frs  0.904278  0.426944 0.4846  0.013 *  
PRP_frs -0.997634  0.068755 0.9433  0.001 ***
RUI_frs -0.648512 -0.761204 0.6243  0.004 ** 
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ 
’ 1 
P values based on 999 permutations.

 
Rémi Lesmerises, biol. M.Sc.,
Candidat Ph.D. en Biologie
Université du Québec à Rimouski
remilesmeri...@yahoo.ca

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