vegan::adonis is deprecated & will be defunct: use vegan::adonis2

[jarioksa]

Description

Latest vegan release 2.6-6 in CRAN deprecates vegan::adonis in favour of vegan::adonis2, and our plan is to make vegan::adonis defunct in the future releases. Building your betadiversity vignette will give a warning with the latest vegan release and will give an error in the future releases (and already in the development version of vegan in github). The fix is obvious: use vegan::adonis2. The new vegan::adonis2 has slightly different internal structure and instead of three list indices (like [[1]][[6]][[1]]) we now must use only two, and there is one column less (so the previous becomes [[5]][[1]]). NB., your original vignette used wrong index for $R^2$ pointing to the p-value. This is also fixed here.

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[adamhsparks]

Many thanks for letting us know about the change (and fixing our mistake too).