One of the projects in the Dynamics and Robotics of Spacecraft Rendezvous and Capture I took at Florida Tech was to make a simulator in Simulink to model proximity operations of two spacecraft.
The model was based around the hill equations and as such modeled the entire state vector of the chaser spacecraft with respect to the target. The choice to use the Hill equations instead of the Clohessy-Wiltshire equations was made to allow for future development to non-circular orbits (although this model so far has only been used for circular orbits). Information about the initial state of the target and chaser spacecraft can be entered into the model as well as a burn schedule for the chaser. The model then runs and will output the chaser state vector as a timeseries.
The class then extended this model to also include perturbation effects on the two spacecraft. Drag and solar radiation pressure were also incorporated as some of the spacecraft perturbations in low Earth orbit. J2 perturbations were also discussed as part of the class but not yet incorporated into the model.
This class also introduced basic spacecraft navigation and Kalman filters. As part of this we also developed a filter using some simulated data and sensors to recover a spacecraft trajectory. This again was implemented in Simulink.