A method of controlling combustion in an homogenous charge compression ignition engine through indirect mechanisms. The method utilizes a predictive model so that combustion can be controlled over a wide range of operating conditions while maintaining optimum operation with respect to efficiency and emissions. The methods include an adaptive aspect, which allows the predictive model to be updated if deemed necessary. Furthermore, the methods include a model with a plurality of control modes. A control mode can be chosen to optimize the engine for one of a plurality of output characteristics, including response time, efficiency, or emissions characteristics.