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.
