adonis is deprecated: use adonis2

[jarioksa]

The next vegan release will deprecate adonis in favour of adonis2. Several CRAN packages have already adopted adonis2 (we have warned on this change since 2016 when adonis2 was released). There are still five CRAN packages that call adonis, but I have contacted their maintainers. For more details, see issue #523. Quick scanning found still more CRAN packages that use adonis, but they do not test those parts and are not caught in CRAN checks. However, these functions will not work correctly. I will have a closer look at these functions after vegan release.

I urge all package maintainers to fix their packages and switch to adonis2. Here an overview of needed changes:

1. The default analysis is now by = NULL instead of by = "terms". For the old result, you must explicitly set adonis2(..., by="terms"). See issue Consider changing the default to by = NULL or by = "margin" in adonis2() #677.
2. If you just call function to get its result, just change adonis() to adonis2() calls.
3. adonis2 return object is essentially the same as the aov.tab element of adonis. Instead of object$aov.tab refer only to object.
4. adonis2 drops column MeanSqs and has one column less (five instead of six), and you must adapt numerical indexing.
5. Some names are slightly modified: SumsOfSqs is now SumOfSqs, and F.Model is now F, and you may need to change named indexing.
6. The return object is now of class anova.cca that inherits from anova or data.frame with attributes (as.data.frame(object) will drop the anova attributes). They are essentially similar as return objects of anova.cca and permutest.cca. There are no longer objects of class "adonis" nor specific methods for that vanished class.
7. adonis2 no longer returns coefficients (for species) and coef.sites . These were based on Euclidean distance, and are misleading (or plainly wrong) with any other dissimilarity (and the choice of dissimilarity did not influence these coefficients). See issue Extracting coefficients #640.