Software

AUC Maximization

"Combining Biomarkers Nonlinearly for Classification uing the Area under the ROC Curve". Fong, Yin, and Huang (2016). Statistics in Medicine, 35(21): 3792-3809. PMCID: PMC4965290. CRAN R package aucm.

RLD: Analyze and Design Repeated Low-Dose Challenge Experiments
Reference: Kang, C., Huang, Y., and Miller, C. (2015) A discrete time-survival model with random effects for designing and analyzing repeated low-dose challenge experiments. Biostatistics, 16(2):295-310. PMCID: PMC4786638. CRAN R package rld Download

Supplementary Material for "Borrowing Information across Populations in Estimating Positive and Negative Predictive Values", Huang, Fong, Wei, Feng, 2011. Journal of the Royal Statistical Society, 60 (5), 633-653, PMCID: PMC3196635.

"Assessing Treatment-Selection Markers using a Potential Outcomes Framework", Huang, Gilbert, and Janes, 2012, Biometrics, 68(3): 687-96. PMCID: PMC3417090. R package tsm_0.0.2.zip (38KB) and tsm_0.0.2.tar.gz (15KB)

"Identifying optimal biomarker combinations for treatment selection via a robust kernel method". Huang and Fong 2014, Biometrics, 70(4): 891-901. PMCID: PMC4277554. R package rts_2.0.tar.gz

"Identifying Optimal Biomarker Combinations for Treatment Selection through randomized controlled trials", Huang 2015. Clinical Trials, 12(4): 348-356. PMCID: PMC4506270. R code and example data for implementing the W-SRAMP-L1 estimator for selecting and combining biomarkers in deriving personalized treatment-selection rule. Rcode: Rcode_CT.zip

"A Method to Address Between-Subject Heterogeneity for Identification of Principal Surrogate Markers in Repeated Low-Dose Challenge HIV Vaccine Studies". Spieker and Huang (2017), Statistics in Medicine, 36(25): 4071-80. PMCID: PMC5669638. Example R code.

"Statistical methods for down-selection of treatment regimens based on multiple endpoints, with application to HIV vaccine trials", Huang, Gilbert, Fu, Janes 2017, Biostatistics, 18(2): 230-243. PMCID: PMC6092735. Zip file for R-code.

"Tree-based Ensemble Methods for Individualized Treatment Rules". Zhu, Huang, and Zhou (2018). Biostatistics & Epidemiology; 2(1): 61-83. PMCID: PMC6812564. Example R code.

"Evaluating the surrogacy of multiple vaccine-induced immune response biomarkers in HIV vaccine trials". Dasgupta and Huang (2020) Biostatistics, kxz039, https://doi.org/10.1093/biostatistics/kxz039R code at Github.

"Identification of the optimal treatment regimen in the presence of missing covariates". Huang and Zhou (2020), Statistics in Medicine, 39(4): 353-368. PMCID: PMC6954309. Zip file for R-code.

"Assessing the increment value of new biomarkers based on OR rules". Wang, Luedtke, and Huang (2020). Biostatistics, 21(3): 594-609. PMCID: PMC7307975. R code at GitHub.

"Evaluation of Treatment Effect Modification by Biomarkers Measured Pre- and Post-Randomization in the Presence of Non-Monotone Missingness". Zhuang, Huang, and Gilbert (2020). Biostatistics, kxaa040, https://doi.org/10.1093/biostatistics/kxaa040R code at Github

"Selecting Biomarkers for Building Optimal Treatment Selection Rules Using Kernel Machines". Dasgupta and Huang (2020). Journal of Royal Statistical Society C; 69(1): 69-88. PMCID: PMC7485396. R code at Github.

"Strategies for Validating Biomarkers Using Data from a Reference Set". Wang, Huang, and Feng (2020). Biostatistics, kxz031, https://doi.org/10.1093/biostatistics/kxz031. The R code is available at https://github.com/WangLu88/ValidationDesign.git.