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.