Hi,

I am trying to run longitudinal linear-mixed-effects, however, due to my nested design, I am getting the error: "Linear model will not compute due to singular matrix error."

I know my "Donation" is dependent of the "Individual" variable, however, I am not sure how to proceed (Donation is a nested factor of Individual). My goal is to be able to generate a volatility plot similar to this (https://www.biorxiv.org/content/10.1101/223974v1.full), where I can plot the change in distance over time, per "Individual".

Here is my code:

qiime longitudinal linear-mixed-effects

--m-metadata-file bray_tp_baseline.qza #output of first-distances

--m-metadata-file meta_long2.tsv

--p-metric Distance #bray

--p-state-column TP #Timepoint 1, 2 or 3 (some samples have 1&2 timepoints, some have 1,2&3 timepoints)

--p-individual-id-column Donation #some individual produce multiple donations, nested factor of Individual

--p-group-columns Individual #different individuals

--o-visualization bray_tp_lme.qzv

metadata :

meta_long2.tsv (929 Bytes)

Any help will be greatly appreciated

Thank you!