DataGeneration_TPD      This code a function that generates a sample Y,
                        Z, G given some initial parameters.
lrtest                  Likelihood ratio test for 'twoPhaseSPML' models
optimTP.GA              Genetic-algorithm optimal phase 2 design for a
                        two-phase genetic association study.
optimTP.LM              Lagrange-multiplier optimal phase 2 design for
                        a two-phase genetic association study.
print.lrtest.twoPhaseSPML
                        Print method for 'lrtest.twoPhaseSPML' objects
print.twoPhaseSPML      Print method for 'twoPhaseSPML' objects
twoPhase                Internal function to optimize over a range of
                        maf, LD and betas.
twoPhaseDesign          Compute sample allocations for a two phase
                        study design.
twoPhaseHeuristic       Select samples for phase 2 under heuristic
                        designs.
twoPhaseSPML            Performs inference on two-phase studies data
                        via semiparametric maximum likelihood.
twoPhaseSPML.control    Auxiliary for Controlling the EM algorithm in
                        twoPhaseSPML.
