The simulated data were designed to have similarities to the real dataset. It was assumed that a complex trait such as alcoholism might have both genetic and environmental risk factors. It was further assumed that such a complex trait might be defined/measured in a variety of different ways by different investigators, have associated endophenotypes that are common in the general population, and is likely to be not one disease but a heterogeneous collection of clinically similar, but genetically distinct, entities. Disease characteristics and parameters were constant throughout all the simulations, but four different "studies" were simulated used varying ascertainment schemes based on differing assumptions about disease characteristics. One of the studies contained multiplex two and three generation pedigrees with at least four affected members. The simulated disease was a psychiatric condition with many associated behaviors (endophenotypes), almost all of which were genetic in origin. The underlying disease model contained four major genes and two modifier genes. The four major genes interacted with each other to produce three different "phenotypes", which were themselves heterogeneous. The population parameters were calibrated so that
