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: ca...@usgs.gov <brian_c...@usgs.gov> tel: 970 226-9326 On Tue, Oct 27, 2015 at 7:42 AM, Sean Porter <spor...@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:ssef...@gmail.com] > Sent: 27 October 2015 03:11 PM > To: Sean Porter > Cc: r-help@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 <spor...@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@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 > ************************************************** > sas0...@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@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@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.