lefse and repeated measures data

[Erica Plummer]

Hi LEfSe forum

Could someone please clarify for me how/if lefse accounts for correlation between repeated measures collected from the same subject when subject ID is specified?  A previous post suggested that 'including a subject variable is a sort of minimal way of introducing pairing to the analysis', but can anyone please expand on this further?  For context, my dataset is from a case control cohort with between 2-4 samples from 100 individuals and I'd like to be able identify features that differentiate cases and controls while controlling for subject ID.

Thank you

Erica