Thank you so much @Nicholas_Bokulich! I appreciate your response.
I continued playing around with the different functions of this plugin, and ended up really liking the pairwise-distances function.
What is the difference between running 3x 'first-distances' analyses each with 2 time points (as you recommended) vs. using the 'pairwise-distance' function like this:
qiime longitudinal pairwise-distances
--i-distance-matrix weighedUniFrac.qza
--m-metadata-file clinical_metadata.tsv
--p-group-column drink . #this is my intervention variable
--p-state-column start_end \ #this is my time variable
--p-state-1 0
--p-state-2 1
--p-individual-id-column BlindedID
--p-parametric True
--p-replicate-handling 'random'
--o-visualization first-distances-pairwise.qzv
**
I also attempted to do as you recommended: 1) filtered my samples to only keep 1 intervention at a time with 2 time points, and made sure that there were in fact 2 time points in my filtered file. 2) running first-distances:
qiime longitudinal first-distances
--i-distance-matrix weighedUniFrac.qza
--m-metadata-file clinical_metadata.tsv
--p-state-column start_end \ time variable
--o-first-distances first-distances.qza
--p-individual-id-column BlindedID
--p-replicate-handling random
then, 3) running linear-mixed-effects on 2):
qiime longitudinal linear-mixed-effects
--m-metadata-file clinical_metadata.tsv
--m-metadata-file first-distances.qza
--p-metric Distance
--p-state-column start_end
--p-individual-id-column BlindedID
--p-group-columns sequence_num,DuringCOVID
--o-visualization first-distances-LME.qzv
And this is the error message I get:
Plugin error from longitudinal:
state_column must contain at least two unique values. Values in start_end: [1.]
Debug info has been saved to /var/folders/ls/344d89x91vn44bb6jrd1qg900000gn/T/qiime2-q2cli-err-e6fj6ifj.log
Probably because 'first-distances' computes the difference in distances between state 0 and state 1, which gives me only 1 variable (=∆ from baseline) - but please confirm if I am misinterpreting something!
Sabrina