[R-sig-eco] Two-way contrasts with adonis()
microbiomics
microbiomics at mytng.de
Tue Mar 8 14:20:18 CET 2016
Dear Alexandre,
I may not have understood what you are up to, but your approach appears
quite strange to me. If you wish to perform a two-way permanova with
interactions, this would be:
fullModel <- adonis(sp ~ treat * imp, method = "euclidean")
fullModel
Call:
adonis(formula = sp ~ treat * imp, method = "euclidean")
Permutation: free
Number of permutations: 999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
treat 2 657.60 328.80 1197.73 0.88707 0.001 ***
imp 1 68.66 68.66 250.12 0.09262 0.001 ***
treat:imp 2 0.23 0.11 0.42 0.00031 0.646
Residuals 54 14.82 0.27 0.02000
Total 59 741.31 1.00000
From this, you can see that the interaction term treat:imp is not
significant. Thus, performing pairwise comparisons for all factor
combinations does not make sense in the first place - it would be enough
to concentrate on the main effects here.
Now, _suppose_ the interaction _was_ significant; then you could do the
following:
For a pairwise comparison "c1" of impyes and impno within treatt1, do:
c1 <- Treat_Imp[, 1] - Treat_Imp[, 2]
adonis(sp[as.logical(c1), ] ~ c1[as.logical(c1)], method = "euclidean")
Repeat the above for treatt2 and treatt3.
As mentioned above, I may be off the track regarding your underlying
purpose, and perhaps others here have better ideas regarding this issue.
Nonetheless, I hope that helps. ;-)
Best,
Sven
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