BMA-POCRM

This repository contains R code to implement and simulate the Bayesian Model Averaged Partial Order Continual Reassessment Method (BMA-POCRM) and related POCRM analyses for dose-combination escalation trials. The codebase includes trial simulations, processing/analysis scripts and helper utilities used to run large simulation studies and produce summary results and plots.

Repository structure

• bma_pocrm_post.R — Core implementation of POCRM and BMA-POCRM functions, single-trial and repeated-trial simulators, incoherency checks, and utilities used across the project.
• analysis/ — Post-processing and analysis scripts that read saved simulation output and compute summary statistics, incoherency analyses, and plotting routines.
  • 2stage_4grid_processing_func.R — Example processing script for 2-stage 4-grid simulation results.
  • Other analysis scripts used to perform scenario analyses and plotting.
• scripts/ — Simulation drivers and helper utilities used to launch simulation runs and batch processing.
  • helpers/ — Lower-level R scripts used by the simulation drivers.
• results/ — Intended output folder where simulation .RData results are stored (empty in the repo; populated after running simulations).

Dependencies

This project is written in R. Key R packages used (as seen in the code) include:

• dfcrm
• nnet
• numDeriv
• tidyverse
• ggdist

Quick start

1. Open the repository in RStudio or start an R session in the project root.
2. Source the core file and inspect available functions:

source("bma_pocrm_post.R")
ls() # inspect available functions

3. Run an example processing script to summarise previously generated results (change file paths as needed). For example:

source("analysis/2stage_4grid_processing_func.R")
# the example script calls run_combination(1) at the bottom; edit parameters if needed

4. To run full simulations, use the driver scripts in scripts/ (for example, scripts/run_4grid_sim_processing.R or the scripts in scripts/helpers/).

License

MIT License. See LICENSE file for details.