[R-sig-eco] Two-way contrasts with adonis()

[ASANTOS]

Dear members,

I try to create Two-way PERMANOVA contrasts using model.matrix() 
function, but I failed with my output in adonis object. I need all 
comparisons with impyes:treatt1, impno:treatt1, impyes:treatt2, 
impno:treatt2, impyes:treatt3 and impno:treatt3 factors, this is 
possible? In my code:

#1st factor
treat <- gl(3, 20, labels = paste("t", 1:3, sep=""))
#2nd factor
imp <- rep(gl(2, 10, labels = c("yes", "no")), 3)
#create a design matrix of the contrasts for "treat" in "imp"
Treat_Imp<-model.matrix(~ imp:treat-1)


#Variables
eff <- sort(rep(1:6, 10))
# add noise:
sp1 = eff + rnorm(60, 0, 0.25)
sp2 = eff + rnorm(60, 0, 0.25)
sp3 = eff + rnorm(60, 0, 0.25)
sp4 = eff + rnorm(60, 0, 0.25)

sp<-cbind(sp1,sp2,sp3,sp4)

require(vegan)

## do the pm-manova with the orthogonal contrasts for imp and treat'
fm <- adonis(sp ~ Treat_Imp,
               method = "euclidean", perm = 999)
fm

Thanks,

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Alexandre dos Santos
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