# Computer programs

### Sun Y, Gilbert PB. Estimation of stratified mark-specific proportional hazards models with missing marks. Scandinavian Journal of Statistics, Theory and Applications (2012) and Gilbert PB, Sun Y. Testing for vaccine efficacy against a spectrum of pathogen sequences in stratified mark-specific proportional hazards models with missing marks, with application to the RV144 HIV vaccine efficacy trial. Journal of the Royal Statistical Society, Series C (2014)

### Finite-Sample Corrected GEE of Population Average Treatment Effects in Stepped Wedge Cluster Randomized Trials [Method of Scott, deCamp, Juraska, Fay, Gilbert, 2014, Statistical Methods in Medical Research

### Gilbert, Yu, and Rotnitzky (2013, Stat Med), ``Optimal Auxiliary-Covariate Based Sampling Design for Semiparametric Efficient Estimation of a Mean or Mean Difference, with Application to Clinical Trials"

### R Code Implementing Gilbert, Rossini, and Shankarappa (2005, Biometrics)

### Compute Simultaneous Confidence Bands for a Log Hazard Ratio over Time [Method of Gilbert, Wei, Kosorok, Clemens (2002, Biometrics)]

### Sensitivity Analysis for Assessing the Causal Effect of Vaccine on Viral Load [Method of Gilbert, Bosch, and Hudgens (2003, Biometrics)]

### Sample Size for Studying Vaccine Effects on Infection in Repeated Low Dose Challenge Studies [Method of Hudgens and Gilbert (2009, Biometrics)]

### The two-sample problem for failure rates depending on a continuous mark: an application to vaccine efficacy [Method of Gilbert, McKeague, and Sun (2008, Biostatistics)]: R package cmprskContin available at CRAN

### Semiparametric efficient estimation for a two-sample treatment effect in a randomized clinical trial, for a quantitative endpoint, a dichotomous endpoint, or a right-censored time-to-event endpoint [For a quantitative endpoint, the method is described in Gilbert et al. (2009, Vaccine)]: R package speff2trial available at CRAN

### Evaluating covariability of amino acid site doubles and triples, and comparing covariability between two groups of amino acid sequences [Method of Gilbert, Novitsky, and Essex, AIDS Research and Human Retroviruses, 2005; 21: 1016-1030]