[R] monte carlo simulations in permanova in vegan package

[stephen sefick]

Look at the permute package. I believe this functionality is there.

Please excuse my brevity; this message was sent from my telephone.
On Oct 27, 2015 10:55 AM, "Cade, Brian" <cadeb at usgs.gov> wrote:

> 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'.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >         [[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.
> >
> >
> >
> >
> >
> >
> >
> > --
> >
> > 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.
>
>         [[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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