stan-cmdstanr-docker

Table of Contents

• Introduction
• Stan
• Docker

Introduction

A Docker image to run Stan, cmdstanr, and brms for Bayesian statistical modelling

Launch an RStudio webserver using bash stan_serve.sh.

Execute docker pull ghcr.io/jbris/stan-cmdstanr-docker:latest or bash docker_pull.sh to pull the image.

To convert the image into a Singularity container, run singularity pull docker://ghcr.io/jbris/stan-cmdstanr-docker:latest or bash singularity_pull.sh.

Stan

The following packages are installed during the image build process:

• Stan
• RStan
• rstanarm
• CmdStan
• brms
• tidybayes
• bayesplot

The brms_within_chain_parallelization.R script can be executed within the Docker container to evaluate whether within-chain parallelization, CmdStan, and brms are working properly.

Docker

This Docker image extends from rocker/tidyverse. Click this link for more information about the Rocker project.

Running the Docker container will launch an RStudio web server. You can access RStudio by visiting localhost:$R_STUDIO_PORT on your web browser. See .env for the defined environment variables.

Running docker-compose will bind a volume, mapping the container’s home directory to a local r_home directory.

See the Dockerfile for the instructions executed during the build of the Docker image.

View docker-compose.yaml to see the definition for the Stan service.

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