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" <ca...@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: 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. [[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.