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]