Two-Phase Genetic Association Study Design and Analysis with Missing Covariates by Design // Provides functionality for designing and analysing two-phase genetic association studies. Phase 1 data usually come from genome-wide association study (GWAS) results and we assume phase 2 data will be part of a targeted genome sequencing or fine-mapping study. At design stage, the package assists in selecting a subset of individuals that will be sequenced for phase 2 via alternative approaches, including a flexible genetic algorithm (GA) for near-optimal designs. Once phase 2 data have been collected, the package implements methods to analyse phase 1 and phase 2 data together using semi-parametric regression models via the expectation- maximization (EM) algorithm. For more details see Espin-Garcia, Craiu and Bull (2018) doi:10.1002/gepi.22099 and Espin-Garcia, Craiu and Bull (2021) doi:10.1002/sim.9211.