Performing Linear Mixed Model


How can I perform a Linear Mixed Effect Model analysis in qiime2 other than using qiime longitudinal LME? I have tried to use this plugin but it seems that it is only suitable for longitudinal trials (as it seems from its name). In my study, we investigated the effect of four treatments on the gut microbial composition of pigs in one period (the time was not of our interest). Now I would like to see how my four treatments and also other factors (e.g. cage, parity, body weight etc) affected the microbiome diversity in tested pigs?
Much appreciated in advance.

Hi @farhad1990!

At this time there are no other methods implemented in QIIME 2 for this.

The plugin (link) isn't strictly for longitudinal studies:

This QIIME 2 plugin supports methods for analysis of time series data, involving either paired sample comparisons or longitudinal study designs.

I spoke with the developers of this plugin, and they suggested that LME might not be the best choice for answering this question - have you had a chance to check out the adonis visualizer?

Keep us posted! :qiime2:


Hi Matthew,

Thank you! I will go for it and let you know in case if I have any issues.
Have a nice weekend.


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