Systems and methods are disclosed in which a time series analysis algorithm is used to analyze inputs such as adjustments a patient has made to the amplitude of stimulation in an implantable stimulator system. The algorithm uses these inputs to predict how the patient would likely adjust the amplitude in the future, i.e. to predict future amplitudes for the patient as a function of time. Preferably, the algorithm determines one or more of an amplitude level, at least one seasonal variation, or at least one trend when predicting the amplitude. This predicted amplitude can then be used to automatically adjust the amplitude of the stimulation provided by the patient's stimulator. The algorithm may only use previous amplitude adjustments to predict the amplitude, other time-varying inputs, or combinations of both.
