Nested LME and Beta group significance

[Stephanieorch (Stephanie Orchanian)]

Hi, I’m trying to run LME and Beta group significance on my data. I want to nest my categories. Is there a way to do this using Qiime2? Thanks.

[colinbrislawn (Colin J Brislawn)]

Hello Stephanie,

For my own notes, here are the two plugins you mention:
https://docs.qiime2.org/2018.2/plugins/available/diversity/beta-group-significance/
https://docs.qiime2.org/2018.2/plugins/available/gneiss/lme-regression/

Looks like the LME regression can take formulas according to this gneiss page. And hopefully these formulas could be nested with an input like:
--p-formula A + A:B
In which the output depends on A and also on B nested within A.

Beta-group-significance does not appear to support these formulas or nested tests.

Colin