[R] monte carlo simulations in permanova in vegan package

[Sean Porter]

Dear colleagues,

 

I am trying to run a PERMANOVA in the vegan package with an appropriate
number of permutations (see example below), ideally 9999. Obviously that
number of permutations does not exists so I would like to use Monte Carlo
permutation tests to derive the probability value, as is done in the
commercial package PERMANOVA+ for PRIMER. How can I adapt my code so that
adonis will do so ? Many thanks, Sean

 

> permanova <- adonis(species ~ time, data = time, permutations=99,
method="bray")

> permanova

 

Call:

adonis(formula = species ~ time, data = time, permutations = 99,      method
= "bray") 

 

Permutation: free

Number of permutations: 99

 

Terms added sequentially (first to last)

 

          Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)   

time       1  0.070504 0.070504  123.65 0.96866   0.01 **

Residuals  4  0.002281 0.000570         0.03134          

Total      5  0.072785                  1.00000          

---

Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

 

 

> permanova <- adonis(species ~ time, data = time, permutations=999,
method="bray")

'nperm' > set of all permutations; Resetting 'nperm'.

 

 

 

 


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