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FloraExam

License: MIT

FloraExam is an R package built with the {golem} framework that provides a Shiny application to explore, score, and visualize Danish flora and vegetation types. This repository hosts both the code for the FloraExam R package and the Docker configuration that allows seamless deployment.

Table of Contents


Overview

FloraExam is designed to help students:

  • Examine flora data with user-friendly Shiny dashboards.
  • Utilize ecological scoring systems (e.g., CSR values, Ellenberg indicator values).
  • Assess species frequency and spatial information.

This application leverages multiple datasets and the companion Artscore package to provide integrated analysis and visualization tools.

Note: A public instance of this app is available at DanishVegetationTypes.


Features

  1. Interactive Shiny App: Built using {golem} for modular and maintainable Shiny code.
  2. Ecological Scoring: Integrates Ellenberg and CSR values for species analysis.
  3. Frequency and Spatial Data: Includes frequency data and spatial distributions of species.
  4. Easy Deployment: Automated Docker builds for easy deployment on Azure or any other containerized environment.

Installation

You can install FloraExam from GitHub. Before installing, ensure you have the remotes package installed.

# install.packages("remotes") # If not already installed

# Install FloraExam directly from GitHub
remotes::install_github("Sustainscapes/FloraExam")

This will also install the FloraExam R package dependencies automatically.


Running the App

Local R Installation

Once FloraExam is installed, you can launch the Shiny app locally:

library(FloraExam)
run_app()

The app will open in your default web browser.

Docker Installation

This repository includes a Dockerfile that is automatically rebuilt on every push to GitHub. To run FloraExam via Docker:

  1. Clone this repository or pull the public image (if available).

  2. Build the Docker image:

    docker build -t floraexam .
  3. Run the Docker container:

    docker run --rm -p 3838:3838 floraexam
  4. Open your web browser at http://localhost:3838 to access the app.


Data Sources

FloraExam relies on several data sources for its functionality:

  1. Ellenberg_CSR dataset

  2. Final_Frequency and SpatialData datasets

  3. artscore

    • Artscore provides scoring functions for ecological analyses used within FloraExam.

These datasets and the artscore package are automatically installed or fetched when you install and run FloraExam (provided you have internet access).


Dependencies

The main additional dependency used by FloraExam is:

  • Artscore: An R package for ecological scoring and analysis.

All other dependencies (R packages) can be found in the DESCRIPTION file within this repo.

artscore Package

The artscore package is developed by Sustainscapes. It includes key functions for calculating ecological indices, scoring species, and more. FloraExam integrates with artscore to enhance your ecological analysis workflow.


Live Demo

A live version of FloraExam is hosted at:
DanishVegetationTypes

Feel free to explore and interact with the app to see what FloraExam can do!


Contributing

We welcome contributions to improve FloraExam. Here’s how you can help:

  1. Fork the repository on GitHub.
  2. Create a new branch for your changes.
  3. Commit and push your changes to your branch.
  4. Submit a Pull Request describing your changes.

Please ensure your code meets our style guidelines and includes unit tests where necessary.


License

This project is licensed under the terms of the MIT License. You are free to use, modify, and distribute this software.


Acknowledgments

We extend our thanks to all contributors and the open-source community who make projects like FloraExam possible. Special thanks to:

  • Sustainscapes for developing FloraExam and the artscore package.
  • The authors and maintainers of the various data repositories integrated into FloraExam.

For any questions or issues, please open an issue or contact us directly.

Happy exploring and analyzing Danish flora and vegetation!

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Shiny app for studying danish flora and vegetation

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