Skip to content

psboonstra/AdaptiveBayesianUpdates

Repository files navigation

R code for the simulation study reported in Boonstra and Barbaro (2018)

This is a companion repository for the R package adaptBayes available at https://github.com/umich-biostatistics/adaptBayes. The adaptBayes package contains the code for actually fitting an adaptive prior in a Bayesian GLM. This repository only contains the additional code needed for conducting the simulation study in Boonstra and Barbaro (2018). Before you can use this repository, you need to first install and load the adaptBayes package using the following commands:

if(!require(adaptBayes)) {
  library(devtools)
  # if installation is necessary, compiling everything will take a few minutes
  install_github('umich-biostatistics/adaptBayes') 
} 

After installing the package, you can use the scripts in this repository to reproduce the simulations studies in the manuscript. See also vignette.pdf for a vignette describing the typical usage of the adaptive Bayesian priors on a simulated dataset

Further details

In more detail, there are six files included in this repository (in addition to this README and vignette.pdf): one text file (run_abu_sims.txt) and five R scripts (ending in .R). The simulation studies reported in Boonstra and Barbaro were run using commit 22

Text file

run_abu_sims.txt is the script for submitting parallel runs of run_aub_sims.R (described below) to a cluster that is running SLURM. The following command run in terminal will do this:

sbatch run_abu_sims.txt

The script assumes that you want all of the results to be put in your home directory (which you probably don't). Edit the script as needed

R files

vignette.R creates a single simulated dataset and walks through analyzing these data using the various adaptive priors. It can also be knit to create a copy of vignette.pdf (it will take a few minutes to knit)

run_abu_sims.R is the script to conduct the large-scale simulation study described in the manuscript. On a local machine, the user may choose a specific array_id (as described in this script's documentation) and run the code locally on his/her machine. On a cluster running SLURM, the user can use this script to submit multiple jobs simultaneously (as described in the description of run_abu_sims.txt above).

functions_simulation.R provides the simulation functions. NOTE: this only contains the extra functions needed to simulate the data; the methods are contained in the adaptBayes package

generate_params.R constructs inputs for running the simulation study. As described in the script's documentation and the language below, these inputs can be overwritten by the user

make_figures.R gives the code to create the figures and tables in the manuscript and supplementary material reporting on the simulation study.

Current Suggested Citation

Boonstra, Philip S. and Barbaro, Ryan P., "Incorporating Historical Models with Adaptive Bayesian Updates" (2018) Biostatistics https://doi.org/10.1093/biostatistics/kxy053

Authors' Copy

DOI for this repository:

DOI

About

R code for the simulation study reported in Boonstra and Barbaro (2018)

Resources

License

Stars

Watchers

Forks

Packages

No packages published