A digital controller includes a sampling component that samples an output signal from a system and an input signal to the system at a first sampling rate, which is at least equal to a predetermined operating rate. An input parameter obtaining component obtains a plurality of input parameters from the samples at the first sampling rate. A decimator component generates subsampled values for the plurality of input parameters at a second sampling rate, which is slower than the first sampling rate. An adaptive plant estimator component generates a model of the system based on the subsampled values. A compensator design component determines compensator parameters based on the model. The compensator parameters reflect changes in the system and are sampled at the second sampling rate. A feedback compensator adjusts the input signal to the system based on the compensator parameters.