Consider changing the default to by = NULL or by = "margin" in adonis2()

[gavinsimpson]

The default permutation test in adonis2() is by = "terms" for a sequential test of model terms where order of terms can matter. I appreciate that this was the default (and only option in adonis()?) but it really isn't very useful in many situations that ecologists will be using adonis2() for (observational data).

by = "margin" would be better if you want a test of model terms by default. by = NULL would be more consistent with the anova() methods for rda(), cca(), etc.

I think we should change this to do the statistically better thing at the expense of backwards "compatability" with adonis().

[jarioksa]

Personally I think that by = "terms" is statistically more correct than by = "margin": single terms sum up to total in sequential tests, but not in marginal tests. I only added that alternative to get rid of whining. That said, I agree with changing the default, but I'd prefer by = NULL.

[gavinsimpson]

This is now implemented in the master branch and in the cran-2.6-6 branches.