1. A computer-implemented method for implementing Fault Detection and Classification (FDC) in an. Advanced Process Control (APC) system including a run-to-run (R2R) controller, the method comprising: receiving an FDC model from memory, the FDC model based on normal tool level parameters; receiving chamber and wafer state data; receiving a process recipe comprising a set of recipe parameters from the R2R controller based on an R2R control model, the R2R control model distinct from the FDC model; providing the process recipe to a process module; providing the FDC model, the chamber and wafer state data, and the process recipe to a process model calculation engine; computing a vector of predicted dependent process parameters using the process model calculation engine based on the provided FDC model, the chamber state and wafer state data and the process recipe; executing the process recipe using only a first wafer of a plurality of wafers in a lot to produce a first vector of measured dependent process parameters; calculating a first difference for the first wafer using the vector of predicted dependent process parameters and the first vector of measured dependent process parameters for the first wafer; comparing the first difference for the first wafer to a threshold value; declaring an alarm condition when the first difference for the first wafer is greater than the threshold value; and displaying alarm condition information on a GUI screen.