[R] monte carlo simulations in permanova in vegan package

[Sean Porter]

Hi Stephen and others,

 

I am trying to run a one-way permanova where I have only 2 levels in the factor “time”, and each level contains only 3 replicates. So because I have such few observations (6 in total) and levels (2) there are not enough possible permutations to get a reasonable test (i.e. (2*3)!/ [2!(3!)^2].   That is why for example if I run the analysis with only 99 permutations it completes the task. However, if I set the number of permutations to anything larger it returns the message “'nperm' > set of all permutations; Resetting 'nperm'.” as the number of possible permutations exceeds the number set by the argument “permutations=”. In PERMANOVA + for PRIMER there is a way of dealing with this issue – by using Monte Carlo simulations to generate the p value with a reasonable number of permutations. Hopefully this clarifies my situation and aim?

 

I was therefore hoping there was a way of coding for the Monte-Carlo permutation procedure into adonis?  

 

Thanks for your help!

 

From: stephen sefick [mailto:ssefick at gmail.com] 
Sent: 27 October 2015 03:11 PM
To: Sean Porter
Cc: r-help at r-project.org
Subject: Re: [R] monte carlo simulations in permanova in vegan package

 

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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Stephen Sefick
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