kamermanpr/docker-pain-variability repository overview

⁠docker-hivsn-variability

A docker image of the R environment required to run the ADVANCE-pain-variability⁠ data analysis scripts.

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⁠R environment

The image is built using the rocker/verse⁠ image of base R⁠ v4.0.2, and includes RStudio server⁠, the TinyTex⁠ Latex distribution, the tidyverse⁠ suite of R packages and several additional R packages that are required to run the scripts in the ADVANCE-pain-variability⁠ GitHub repository.

⁠Added packages

• skimr
• ggforce
• patchwork
• ggthemes
• ggalluvial
• janitor

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⁠Using Docker to run the scripts

You need to have docker installed on your computer. To do so, go to docker.com⁠ and follow the instructions for downloading and installing Docker for your operating system. Once docker has been installed, follow the steps below, noting that docker commands are entered in a terminal window (Linux and OSX/macOS) or command prompt window (Windows).

⁠Download the latest image

Enter: docker pull kamermanpr/docker-pain-variability:v1.3

⁠Run the container

Enter: docker run --name pain -d -p 8787:8787 -e USER=user -e PASSWORD=password kamermanpr/docker-pain-variability:v1.3

⁠Login to RStudio Server

• Open a web browser window and navigate to: localhost:8787

• Use the following login credentials:

  • Username: user
  • Password: password

⁠Upload repository

• Go to the ADVANCE-pain-variability⁠ repository on GitHub and select download as a zip file.

• In the Files tab on the lower right panel of RStudio, click Upload, located the zip file you downloaded and the click OK. The zip file will be uploaded and will automatically unzip, giving you access to all the content, including the analysis scripts, for the project.

• In the Files tab, double-click the ADVANCE-pain-variability.Rproj file to ensure all the working directories are in order before running any of the scripts.

Note: The first time you knit one of the Rmd files, the generation of the PDF output will take some time as tinyTex will install all the required LaTeX packages for generating PDF documents.

⁠Shutting down

Once done, log out of RStudio Server and enter the following into a terminal to stop the docker container: docker stop pain. If you then want to remove the container, enter: docker rm pain. If you also want to remove the docker image you downloaded, enter: docker rmi kamermanpr/docker-pain-variability:v1.3