[R-sig-eco] adonis and contrasts

[Christine Griffiths]

Dear All,

I have done pairwise comparisons of species compositions between three 
treatments (1 v 2, 1 v 3, and 2 v 3) which were replicated 6 times (i.e. 6 
blocks). To avoid multiple testing I have decided to use contrasts instead 
(treatments 1 v 2 + 3, and 2 v 3). Oksanen (2009) mentions that this can be 
done, but when I have tried to incorporate the contrasts, either it doesn't 
run or the output suggests that the contrast has not been addressed.

Below is an example of the model I ran before wanting to add a contrast:

m1<-adonis(dat~Treatment,data=datenv,strata=datenv[,"Block"],permutation=1000,method="bray")

How do I add the following contrasts into the above model?
treatment<-as.factor(Treatment)
contrasts(treatment)<-cbind(c(-2,1,1),c(0,-1,1))
contrasts(treatment)

		[,1] [,2]
1.Control   -2    0
2.Radiata    1   -1
3.Aldabra    1    1

If this is not possible, is it acceptable to sum the species presence in 
the grouped treatments (2 + 3) and divide by 2, then combine this data to 
that of treatment 1 to form a matrix? However, as I would not be able to do 
more than one contrast, then I don't really overcome the problem of 
multiple testing.

I hope this makes sense. Many thanks in advance for any assistance.

Cheers Christine