Perspective plot of the log likelihood surface of the simulation pedigree data with γ = 0.188. The simulated pedigree dataset is generated assuming penetrance values 0.95, 0.7, and 0, and disease allele frequency 0.0001. The likelihood of the simulated pedigree data is evaluated with frequency assigned to 0.0001, and the penetrances are estimated by the MLEP package. Fixing γ at its estimate 0.188, the log likelihood surface is drawn on a limited region reflecting the parameter constraint α ≥ β. The maximum appears near those of the other two maximum likelihood estimates (α,β) = (0.970,0.943).