[R] monte carlo simulations in permanova in vegan package

stephen sefick ssefick at gmail.com
Tue Oct 27 14:10:44 CET 2015


The example code works, and reports 9999 permutations. Can you provide more
information?

data(dune)
data(dune.env)
adonis(dune ~ Management*A1, data=dune.env, permutations=9999)



On Tue, Oct 27, 2015 at 3:56 AM, Sean Porter <sporter at ori.org.za> wrote:

> 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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>
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-- 
Stephen Sefick
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Auburn University
Biological Sciences
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http://www.auburn.edu/~sas0025
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