[R] monte carlo simulations in permanova in vegan package

[Cade, Brian]

Sean:  There are only 20 possible combinations, 6!/(3! x 3!), so you just
need to enumerate them completely (no Monte Carlo approximation required).
I don't know if permanova() can do this but you can do it with the mrpp()
functions and argument (,exact=TRUE) in Blossom package for R.

Brian

Brian S. Cade, PhD

U. S. Geological Survey
Fort Collins Science Center
2150 Centre Ave., Bldg. C
Fort Collins, CO  80526-8818

email:  cadeb at usgs.gov <brian_cade at usgs.gov>
tel:  970 226-9326


On Tue, Oct 27, 2015 at 7:42 AM, Sean Porter <sporter at ori.org.za> wrote:

> 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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>
> ______________________________________________
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
>
>
>
>
>
> --
>
> Stephen Sefick
> **************************************************
> Auburn University
> Biological Sciences
> 331 Funchess Hall
> Auburn, Alabama
> 36849
> **************************************************
> sas0025 at auburn.edu
> http://www.auburn.edu/~sas0025
> **************************************************
>
> Let's not spend our time and resources thinking about things that are so
> little or so large that all they really do for us is puff us up and make us
> feel like gods.  We are mammals, and have not exhausted the annoying little
> problems of being mammals.
>
>                                 -K. Mullis
>
> "A big computer, a complex algorithm and a long time does not equal
> science."
>
>                               -Robert Gentleman
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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