Hello everyone can somebody tell me how I can control for nestedness in the adonis2 model? Site is nested with forest and I thought this was the way to do it, but if remove everything after method="bray", the result of the model is the same as with perm=how() and plots=plots(). Results:
adonis2(formula = bird.dist ~ forest, data = bird_data, permutations = 999, method = "bray")
Df SumOfSqs R2 F Pr(>F)
forest 1 40.215 0.19859 131.58 0.001 ***
Residual 531 162.286 0.80141
Total 532 202.501 1.00000
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Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
The code:
bird.dist<-vegdist(bird.matrix, method='bray')
bird.div<-adonis2(bird.dist~forest, data=bird_data, permutations = 999, method="bray",
perm= how(blocks = bird_data$forest,
plots = plots(strata = bird_data$site)))```