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.