Developing a reproducible Shiny app

Example Shiny application adopting the recommendations of "Ten Quick Tips for Developing a Reproducible Shiny Application", Brun et al, 2025, PLOS Computational Biology.

In this example, we are reusing the Faithful Shiny app example provided as part of the R shiny package. This Shiny application displays eruption duration in minutes for the Old Faithful geyser.

Tips demonstrated

• Set up your computing environment
  • Use git and GitHub
  • Use renv to record package versions
  • Record the output of sessionInfo()
• Document and develop incrementally
  • Comment UI elements
• Make your Shiny application modular and portable
  • Organize code and data
  • Use relative paths and file.path
• Preprocess and cache data for performance
  • Cache remotely-accessed and processed data in a local file
• Make underlying data accessible
  • Cite the original data
• License code and data appropriately
  • Add a LICENSE file
  • Respect the license of the original data
• Make your data and source code citable
  • Add a suggested citation to the README
  • Add a CITATION.cff file
• Share your app
  • Publish on shinyapps.io and archive in Zenodo

How to run this Shiny app

1. Clone this repository and run at the R console: shiny::runApp()
2. At the R console run: shiny::runGitHub(repo="shiny-qt-example", "UCSB-Library-Research-Data-Services")

File structure

This repository has the following file structure:

├── CITATION.cff
├── data
│   ├── faithful_data.csv
│   └── metadata.md
├── global.R
├── LICENSE
├── README.md
├── renv
│   ├── activate.R
│   ├── library
│   ├── settings.json
│   └── staging
├── renv.lock
├── server.R
├── sessionInfo.txt
├── shiny-qt-example.Rproj
└── ui.R

Shiny app

• global.R: Load libraries and check for existing data files
• server.R: server side functions of the Shiny app used to compute the histogram plot and other plot features
• ui.R: user interface of the Shiny app

Virtual computing environment

This app uses renv to create a virtual environment

• renv.lock: list of the R packages used by the virtual environment
• .Rprofile: ensures that the library is used every time you open that project
• renv/activate.R: R script sourced by .Rprofile to activate the virtual environment
• renv/settings.json: virtual environment settings

Data

• faithful_data.csv: CSV file version of the faithful data from the datasets R package
• metadata.md: metadata information about faithful_data.csv

References

The underlying data is available as part of R package datasets. The version used is distributed with R 4.5.0. This version is a simplification of the original data collected by Azzalini, A. and Bowman, A. W. (1990). See metadata.md in the data directory for more information.

Cite this work as: Brun, J., Janée, G., & Curty, R. G. (2025). Example Shiny application adopting the recommendations from "Ten Quick Tips for Developing a Reproducible Shiny Application" [Computer software]. https://github.com/UCSB-Library-Research-Data-Services/shiny-qt-examples