Abstract: The combined effects of a selected treatment option on multiple causes of morbidity or mortality are simulated for evaluation. Various patient-specific and model-specific parameters, including parameters related to diseases to be modeled, are used in modeling incidence and mortality rates for each disease. These disease-specific models are used for defining a set of health states having initial probabilities, which are used to formulate a transition matrix used in matrix calculation to obtain output matrix Q. If additional cycles are needed, the transition matrix is updated and matrix calculation is performed using the updated transition matrix. Otherwise, final output matrix Q is utilized for calculation of values needed for determining an overall treatment score. The calculated values and/or values from Q are combined with patient or numeric scores from other treatment choice-related domains to obtain a raw score that is used to produce a patient-specific score for a selected treatment option.