This repository contains R code for implementing the generalized calibrated Bayesian hierarchical (GCBHM) design.
- code_for_rerunning_simu/: R code necessary for rerunning the simulations presented in the manuscript.
- code_for_tables_figures/: R code for reproducing all the tables and figures featured in the main paper and supplementary materials.
- Rdata/: This directory stores saved intermediate results in Rdata files from our simulations. These files are used for reproducing the tables and figures presented in the paper.
- Results/ ALL tables and figures presented in paper.
- master.R: This file serves as a summary, providing an overview of the code needed to reproduce the results.
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 14.0
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_1.1.1 ggtext_0.1.1 ggplot2_3.4.3 RColorBrewer_1.1-3 dplyr_1.1.2
[6] reshape_0.8.8 doParallel_1.0.17 iterators_1.0.14 foreach_1.5.2 runjags_2.2.0-3
[11] R2jags_0.7-1 rjags_4-14 coda_0.19-4
loaded via a namespace (and not attached):
[1] Rcpp_1.0.10 pillar_1.9.0 compiler_4.1.2 plyr_1.8.6 tools_4.1.2
[6] boot_1.3-28.1 lifecycle_1.0.3 tibble_3.2.1 gtable_0.3.1 lattice_0.20-45
[11] pkgconfig_2.0.3 rlang_1.1.1 cli_3.6.0 rstudioapi_0.15.0 xml2_1.3.3
[16] withr_2.5.0 generics_0.1.1 vctrs_0.6.3 gridtext_0.1.4 grid_4.1.2
[21] tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.3 magrittr_2.0.3
[26] scales_1.2.1 codetools_0.2-18 R2WinBUGS_2.1-21 abind_1.4-5 colorspace_2.0-3
[31] utf8_1.2.2 munsell_0.5.0
Chi, X., Yuan, Y., Yu, Z., and Lin, R.* (2024). A Generalized Calibrated Bayesian Hierarchical Modeling Approach to Basket Trials with Multiple Endpoints. Biometrical Journal.