Hi Andy,
Please excuse the late reply. Have you looked into using sbiosampleparameters? This function allows you to sample your covariate model with the thetas and etas you have estimated. The covariate model, the estimated thetas and etas can all be extracted from your Mixed effects fit results (NLMEresults object). In addition, you will need to create a dataset that contains the regressors for each subject that you want to simulate.
Once you have sampled your covariate model with the estimated thetas and etas, you can then simulate your model using the a simfunction. I recommend calling the simfunction with an outputTimes vector instead of a stopTime, in order to get homogeneous output vectors for each simulation. This is a requirement for calculating percentiles, see below.
Once you have simulated your samples, you can use the prctile function to calculate the percentiles. For the visualization of percentiles, you might want to have a look at visualization methods, perhaps on the MATLAB FileExchange here.
Let me know if this answers your question.
Best,
Sietse
