| aco1arm | A function to estimate parameters in augmented case-only designs, the genotype is ascertained for a random subcohort from the active treatment arm or the placebo arm. |
| aco2arm | A function to estimate parameters in Cox proportional hazards model using augmented case-only designs, the genotype is ascertained for a random subcohort from both the active treatment arm and the placebo arm (case-cohort sampling) or a case-control sample in both arms. |
| acoarm | A function to estimate parameters in Cox proportional hazard models by augmented case-only designs for randomized clinical trials with failure time endpoints. |
| acodata | A dataset from the STEP trial to study the interactions between gene and vaccine on HIV infection |
| caseonly | A function to deal with case-only designs |
| char2num | A function used in acoarm to transform categorical variable to integers |
| mele | function to compute the maximum estimated likelihood estimator |
| remove_missingdata | A function used in acoarm to remove missing data |
| remove_rarevariants | A function used in spmle and acoarm to remove rare-variant covariates |
| spmle | function to compute the semiparametric maximum likelihood estimator |
| whiBioMarker | An example dataset to demostrate the usage of MELE and SPMLE |