A diesel engine (10) operates by alternative diesel combustion. Formation of fuel and charge air mixtures is controlled by processing a particular set of values for certain input data according to a predictor algorithm model (50) to develop data values for predicted time of auto-ignition and resulting torque, and also develop data values for control of fuel and air that will produce the predicted time of auto-ignition and resulting torque. The data values developed by the predictor algorithm and data values for at least some of the input data are processed according to a control algorithm (52) that compensates for any disturbance introduced into any of the data values for at least some of the input data being processed by the control algorithm. This causes the systems to be controlled by compensated data values that produce predicted time of auto-ignition and resulting torque in the presence of any such disturbance.