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

[microbiomics]

On 09.03.2016 12:34, ASANTOS wrote:
> Thanks you very much Sven,
>
>            But I try to make multiple comparisons and not with isolate
> factors and doesn't work. In my new code I have significant interaction,
> my example was:
>
> #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
> sp1_1 = rnorm(10, 5, 0.25)
> sp1_2 = rnorm(50, 2.5, 0.25)
> sp1 = c(sp1_1,sp1_2)
> sp2 = rnorm(60, 2.5, 0.25)
> sp3_1 = rnorm(10, 12, 0.25)
> sp3_2 = rnorm(50, 2.5, 0.25)
> sp3 = c(sp3_1,sp3_2)
> sp4 = rnorm(60, 2.5, 0.25)
> sp<-cbind(sp1,sp2,sp3,sp4)
>
> require(vegan)
>
> fullModel <- adonis(sp ~ treat * imp, method = "euclidean")
>
> fullModel
>
> #Comparisons
> impyes:treatt1_impno:treatt1<- Treat_Imp[, 1] - Treat_Imp[, 2]
> impyes:treatt2_impno:treatt2<- Treat_Imp[, 2] - Treat_Imp[, 3]
> impyes:treatt3_impno:treatt3<- Treat_Imp[, 3] - Treat_Imp[, 4]
>
> adonis(sp ~
> impyes:treatt1_impno:treatt1[as.logical(impyes:treatt1_impno:treatt1)]
> +impyes:treatt2_impno:treatt2[as.logical(impyes:treatt2_impno:treatt2)]+
> +impyes:treatt3_impno:treatt3[as.logical(impyes:treatt3_impno:treatt3)],method
> = "euclidean")
> #
>
>
>