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https://github.com/jbris/stan-cmdstanr-docker

A Docker image to run Stan, cmdstanr, and brms for Bayesian statistical modelling
https://github.com/jbris/stan-cmdstanr-docker

bayesian-inference bayesian-statistics bayesplot brms cmdstan data-science docker docker-compose docker-image dockerfile probabilistic-programming r rstan rstanarm stan statistics tidybayes tidyverse

Last synced: 2 months ago
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A Docker image to run Stan, cmdstanr, and brms for Bayesian statistical modelling

Host: GitHub
URL: https://github.com/jbris/stan-cmdstanr-docker
Owner: JBris
License: mit
Created: 2022-07-26T11:45:57.000Z (over 2 years ago)
Default Branch: main
Last Pushed: 2024-02-19T07:59:19.000Z (11 months ago)
Last Synced: 2024-02-19T08:54:15.707Z (11 months ago)
Topics: bayesian-inference, bayesian-statistics, bayesplot, brms, cmdstan, data-science, docker, docker-compose, docker-image, dockerfile, probabilistic-programming, r, rstan, rstanarm, stan, statistics, tidybayes, tidyverse
Language: Dockerfile
Homepage: https://jbris.github.io/stan-cmdstanr-docker/
Size: 28.3 KB
Stars: 7
Watchers: 3
Forks: 4
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md

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README

        # stan-cmdstanr-docker

[![pages-build-deployment](https://github.com/JBris/stan-cmdstanr-docker/actions/workflows/pages/pages-build-deployment/badge.svg?branch=main)](https://github.com/JBris/stan-cmdstanr-docker/actions/workflows/pages/pages-build-deployment)

## Table of Contents  

* [Introduction](#introduction) 

* [Stan](#stan) 

* [Docker](#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](https://mc-stan.org/)

* [RStan](https://mc-stan.org/users/interfaces/rstan)

* [rstanarm](https://mc-stan.org/rstanarm/)

* [CmdStan](https://mc-stan.org/users/interfaces/cmdstan)

* [brms](https://paul-buerkner.github.io/brms/)

* [tidybayes](https://mjskay.github.io/tidybayes/)

* [bayesplot](https://mc-stan.org/bayesplot/)

The [brms_within_chain_parallelization.R](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.](https://rocker-project.org/images/)

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](.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](Dockerfile) for the instructions executed during the build of the Docker image. 

View [docker-compose.yaml](docker-compose.yaml) to see the definition for the Stan service.