Adonis2 output not showing factors correctly (only "model")

[kingmicro]

Hello everyone,

I have been having some issues with adonis2. In the past, when I have used adonis2 I would input a formula (e.g. A*B) and I would get a breakdown of: A, B, A:B. Recently, I am running some adonis2 for other data and the output only gives “model”

adonis2(formula = MainPassage_16S_Bray ~ Gen * Sample * Treatment2, data = metadata_MainPassage_16S)
Df SumOfSqs R2 F Pr(>F)
Model 65 56.552 0.77242 12.845 0.001 ***
Residual 246 16.662 0.22758
Total 311 73.213 1.00000

I talked to some colleagues of mine and they said they had the same issue a couple of months back and couldn’t fix it. Has something changed in the last couple of updates that no longer show the individual factors in the output?

When I run the code using the Dune data, I also receive the same output

data(dune)
data(dune.env)
adonis2(dune ~ Management*A1, data = dune.env)

adonis2(formula = dune ~ Management * A1, data = dune.env)
Df SumOfSqs R2 F Pr(>F)
Model 7 2.4987 0.58122 2.3792 0.001 ***
Residual 12 1.8004 0.41878
Total 19 4.2990 1.00000

I am running Vegan version 2.6.8. Has anyone else had similar issues and can someone please advise a way forward?

Thanks!

[kingmicro]

Hello everyone - just in case others need to find a fix it is because the default parameters were changed. You need to include by = "terms"

[jarioksa]

Yes indeed, this is a duplicate of #694