I want to ask how confidence intervals are calculated for a given simulation. For example for MassiveMIMO Scenario, the graph contains some large intervals and some small one in terms of length of Intervals? does that mean something different or its just the same thing?
The confidence intervals are calculated via bootstrapping. This is performed in +Results/SimulationsResults.m by calling the function Utils.Extras.bootci.
By default, a 95% confidence level is used when calling that function. You can find some details here: https://en.wikipedia.org/wiki/Confidence_interval .
Roughly speaking, they indicate the accuarcy of your simulated results. Large confidence intervals correspond to uncertain results, meaning that if you repeat the simulation, you are less likely to get a similar average value (of the throughput for example). In order to make them smaller, and therefore make the results more accurate and representative, you should increase the number of simulation samples by increasing the number of simulated frames, i.e., set scStr.simulation.nFrames to a larger value in the scenario file.