[R] adonis (vegan package) and subsetted factors

[tyler]

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