software

• R package and example for "U-Bayes: Bayesian Safety and Futility Monitoring in Phase II Trials Using One Utility-based Rule" by Lee, and Thall (2023, submitted)

  • Vignette

  • Zip file that includes R package "U-Bayes" and Example code with a readme file

• R package and example for "Bayesian Modeling of Interaction between Features in Sparse Multivariate Count Data with Application to Microbiome " by Zhang, Shen, Chen,  and Lee (2023)

  • Link for S. Zhang's GitHub: R package "SP-BGMF" and Example code with a readme file

• R package and example for "Bayesian Treatment Screening and Selection Using Subgroup-Specific Utilities of Response and Toxicity" by Lee, Thall and Msaouel (2023)

  • Zip file that includes R package "Screen-Subgroup" and Example code with a readme file

• R package and example for "Utility Based Bayesian Personalized Treatment Selection for Advanced Breast Cancer" by Lee, Thall, Lim and Msaouel (2023)

  • R package "UtilityBasedAnalysis" 

  • Example code to reproduce the simulation results in Section 4

  • RData that has the simulated data and simulation truth

• R package and example for "Precision Bayesian Phase I-II Dose-Finding Based on Utilities Tailored to Prognostic Subgroups" by Lee, Thall and Msaouel (2021) in Statistics in Medicine

  • R package "DoseFindingSubgroup"

  • Example of performing one time inference

  • Example of performing the simulations in the paper - our proposed design

  • Example of performing the simulations in the paper - our comparators (D-Comb and D-Sub)

• R package and example for "A Bayesian Nonparametric Analysis for Zero Inflated Multivariate Count Data with Application to Microbiome Study" by Shuler, Verbanic, Chen and Lee (2021) in JRSS-C

  • R package bnpzimnr with an example.

• R package and example for "A Phase I-II Design Based on Periodic and Continuous Monitoring of Disease Status and Times to Toxicity and Death" by Lee, Thall and Msaouel in Statistics in Medicine (2020)

  • R package and R script to reproduce simulations in the manuscript.

• R package and example for "Bayesian Sparse Multivariate Regression with Asymmetric Nonlocal Priors for Microbiome Data" by Shuler, Sison-Mangus and Lee in Bayesian Analysis (2019)

  • R package anlpsb with an example.

  • Paper

• R package and vignette for "Joint Bayesian Semiparametric Regression Analysis of Recurrent Adverse Events and Survival" by Lee et al in the Annals of Applied Statistics (2019)

  • vignette pdf file

  • R package

  • Example simulated data RData file

  • Example R code

  • Paper

• R package and example for "Optimizing Natural Killer Cell Doses for Heterogeneous Cancer Patients Based on Multiple Event Times" by Lee et al in JRSS-C (2019)

  • R package and R script to run a simulation study under Scenario 1 in the manuscript.

  • Paper

• R package and example for "A Bayesian Semiparametric Regression Model for Joint Analysis of Microbiome Data" by Lee and Sison-Mangus in Frontiers in Microbiology (2018)

  • R package and R script to reproduce Simulation 1 in the manuscript.

  • Paper

• R package BayClone2 for "Bayesian Inference for Intra-Tumor Heterogeneity in Mutations and Copy Number Variation" by Lee et al (2015)

If you need other codes used for my papers, please contact me via email.