On Thu, Apr 10, 2008 at 04:47:44PM +0100, Gavin Simpson wrote: > > This behaviour arises from the following, using the in-built dune data: > > > newdune.env <- subset(dune.env, Management != "NM") > > newdune.env$Management > [1] BF SF SF SF HF SF HF HF BF BF HF SF SF HF > Levels: BF HF NM SF > > Notice this hasn't dropped the empty level "NM", and this is what is > catching out adonis --- it is not checking for empty levels in the > grouping factor, as this shows: > > > newdune <- dune[which(dune.env$Management != "NM"), ] > > adonis(newdune ~ Management*A1, data=newdune.env, permutations=100) > > Call: > adonis(formula = newdune ~ Management * A1, data = newdune.env, > permutations = 100) > > Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) > Management 3.00000 0.57288 0.19096 1.27735 0.2694 <0.01 *** > > For now, forcibly remove empty factor levels as per your second example, > but I'll take a look at fixing adonis()
Great, thanks! Tyler ______________________________________________ R-help@r-project.org mailing list 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.