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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