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vegandevs / vegan Public

about betadisper() interpretation #483

Unanswered Gian77 asked this question in Q&A Feb 2, 2021 · 2 comments Something went wrong. Quote reply Feb 2, 2021

I I am using the function betadisper() after adonis() to test for homogeneity of variances. I have used it a lot in the years but I never get to look at the boxplots output with the necessary attention.

So this is my code.

permdisp



In the ordination plot looks like the Root samples should have smaller distances to centroids respect to the Soil samples. However, this is not what we see int he boxplot. is it because the PCoA is in 2D but in reality there are many axes, so the distances to the centroids might be bigger than what seen in PC1 & PC2.
So I tried to plot the distance manually and I got this

SAM110 SAM111 SAM37 SAM112 SAM113 SAM114 SAM115 SAM116 SAM117 SAM118 SAM119 SAM120 Root Root Root Soil Soil Soil Soil Root Root Root Root Soil Levels: Root Soil
Levels 1 and 2 correspond exactly to Root and Soil. This plot makes more sense to me in relation to the PCoA graph. 
So, I am wondering if:

  does the default function boxplot() on the betadisper object (as showed above) calculates distance distribution across all axis?
  does the boxplot() plotted manually actually show the distances seen in the 2D PCoA?
  Does then anova [ anova(permdisp, permutations = 9999) ] used tests for differences across group centroids using all PCoA axis or just the first 2?

Thanks you very much,
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