I'm re-entering the world of SEM after a hiatus and slowly familiarising myself with OpenMx (previous Mx user). I've successfully implemented some simple uni- and bi-variate VC models for some of our latest twin data (microbiome phenotypes) using the umx packages.
We have longitudinal samples at three time points which I plan to work up a simplex model for. Prior to doing this, I would like some advice on our data structure. For each individual, we have two technical replicates for time points 1 and 2 (taken on consecutive days at T1 and T2), and then two more technical replicates at time point 3, but taken from different sites rather than at different times. For each person, data structure looks like this:
T1 T2 T3
Day 1/Day 2 Day 1/Day 2 Site 1/Site 2
Six samples per person total. Ideally I would like to leverage the replication to tighten CIs without drawing any inference about Day or Site - we have already established that there is no overall influence on phenotype at each time point. How would I best address this in my model? Not looking for syntax specifically (but happy to use any provided), but more guidance on how to treat the data itself.
Thanks in advance.
Toby.