Understanding Z with MERF function

[CBroedlow]

Hello,

I am trying to understand how to use the z matrix with the MERF function. I have 12 biomarkers repeated over 3-time points (baseline,1 month, and 6 months) and would like to use the biomarker concentrations to try and predict my outcome, the number of times a participant had the infection state. Everything I have read online uses a matrix of all 1s with the number of rows equal to my predictor matrix. I want to have z as (1|PID) + (1|PID: days) but I am very confused about how to do that with a matrix.

Also, I have only gotten the function to work when y is numeric and I would prefer to use a categorical response. Does y need to be numeric or am I doing something wrong?