# Computer programs

### R code implementing the Rotnitzky and Robins (1995, Biometrika) Augmented Inverse probability Weighted estimator of a mean and mean difference with application to analyzing peptide microarray outcomes in HVTN 106.

### Price BL, Gilbert PB, van der Laan MJ. R code for implementing the Application for dengue vaccine efficacy trials (on dummy data sets) in "Estimation of the Optimal Surrogate Based on a Randomized Trial" (2018, in press).

### Gilbert PB, Zhang L, Thommes E, Huang Y. R code for implementing the statistical methods described in
"Assessing Pharmacokinetic Marker Correlates of Outcome, with Application to Antibody Prevention Efficacy Trials" (2018, submitted).

### Gilbert PB, Janes HE, Huang Y. Power/Sample Size Calculations for Assessing Correlates of Risk in Clinical Efficacy Trials. Statistics in Medicine (2016).

library(CoRpower)
library(help="CoRpower")
help("computepower")
help("computepower.n")
Additional code for plotting the results of the sample size and power calculations for the first illustration in the manuscript
Additional code for plotting the results of the sample size and power calculations for the second illustration in the manuscript

### Juraska M, Gilbert PB. Mark-Specific Hazard Ratio Model with Missing Multivariate Marks. Lifetime Data Analysis (2016).

### Fu R, Gilbert PB. Joint Modeling of Longitudinal and Survival Data with the Cox Model and Two-Phase Sampling. Lifetime Data Analysis (2016).

### 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 (2014, Statistics in Medicine), ``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]