For first-distance LME, what does Distance refer to? I’m looking at c-section and vaginal data. I made my --p-baseline 1. Is the intercept p-value comparing my first vaginal and c-section samples to each other or comparing it to their baseline 1 value? Thanks.
So then distance is a patient's distance between timepoint X and time 1.
The intercept would indicate whether individuals have different "baseline" values (in this case, whether individuals change at different rates between time 1 and time 2). The p-value for "Delivery mode" would indicate whether baseline values differ by delivery mode.
I hope that helps!
Great, thank you Nicholas. I really appreciate your help.
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When comparing to --p-baseline 1, is this comparing vaginal time point x to vaginal time point 1 and c-section time point x to c-section time point 1? Or is it comparing their time points to the average of their time point 1? Thank you!
Hi there @Stephanieorch!
It is not quite either of those options - the first distances are calculated from within an individual's own sample (whether or not baseline is used). So by setting the baseline parameter, it is comparing the subject to themselves, at the baseline time specified. This would look like subject A's samples from time point 2, compared to time point 1. Then, subject A's samples from time point 3, compared to time point 1, etc., ad nauseum.
Check out this section of the q2-longitudinal tutorial for a bit more detail. Hope that helps! 
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