eLTER SO Costs web application
Quick Links
Access policy :balance_scale:
- This project is open and freely available for use under the terms of the CC0 1.0. For more information about the access rights and usage policies, please refer to the license file.
Context and aims :book: :dart:
This repository hosts the information used to build the eLTER SO Costs web application. This tool is a specialized resource designed to assist the eLTER (European Long-Term Ecosystem Research) community in estimating the costs associated with upgrading and operating standard observations across various eLTER sites.
The essence of this tool lies in its ability to adapt calculations based on unique site-specific criteria, ensuring tailored cost estimations. Key factors taken into consideration include the site category, the habitats, the focus spheres, and the potential co-location with other Research Infrastructures, which cover the costs of specific standard observations.
The goal of this tool is to provide a user-friendly, efficient, and reliable means for the eLTER community to plan and allocate resources effectively.
Input data :floppy_disk:
The input data was built based on the agreement of the eLTER
community regarding the standard observations. The data is located at
the data folder and contains consensus information on the
target sampling protocols, equipment, as well as estimations on the
costs associated to upgrade and operate the standard observations.
Structure of files :open_file_folder:
├── .github # Folder containing information how to interact with the repository on GitHub
│ ├── bug_report.md # Instructions to bug reporting
│ ├── feature_request.md # Instructions to fearure requesting
│ ├── CODE_OF_CONDUCT.md # Information on the code of conduct of the repository
│ └── CONTRIBUTING.md # Instructions to contribute to this repository
├── data # Folder for input data used by the app
│ ├── eLTER-SO-costs_list-of-standard-observations.xlsx # Data file in xlsx format
│ └── eLTER-SO-costs_standard-observations-detailed-costs_V18.csv # Data file in csv format
├── www # Folder containing web assets
│ ├── eLTER-SO-costs_landing-page-picture.jpg # Picture for the web application landing page
│ ├── eLTER-SO-costs_elter-logo.png # eLTER simplified logo in png format
│ ├── eLTER-SO-costs_application-logo.jpg # SO Costs logo in jpg format
│ └── eLTER-SO-Costs_app-webinar-20240328_v1.0.0.pdf # slide presentation introducing the application
├── app.R # The main application script for the Shiny web app
├── .Rprofile # R project-specific configuration file
├── eLTER-SO-costs-App.Rproj # RStudio project file
├── .gitignore # Lists files to be ignored by version control system
├── LICENSE # The full text of the license for the project
├── README.html # Compiled HTML from README.md for detailed project information
├── README.md # Markdown text providing an overview of the project
├── CITATION.cff # Information on how to cite the repository
├── renv # R environment setup with reproducibility in mind
│ └── ... # folders and files by renv to compile the needed information for reproducibility
└── renv.lock # Lock file to capture the state of the R environmentDevelopment :man_technologist:
The web application is coded entirely in the R programming language, with a
user interface developed using R Shiny. R
Shiny is a powerful framework for building interactive web
applications directly from R scripts, making it an ideal choice for
creating accessible and user-friendly tools.
Web application workflow :gear:
- Initial setup and library loading
- The app begins by installing necessary R packages and loading them into the session. This ensures that all required functions and UI elements are available for use.
- Data preparation
- Reads and processes two datasets
- one detailing the costs associated with Standard Observations (SOs) and another providing metadata on SOs. The app performs cleaning, filtering, and merging operations to prepare the data for analysis.
- Reads and processes two datasets
- User Interface (UI) construction
- Constructs a web interface with multiple tabs and input options. Users can navigate through these tabs to input specific parameters related to their site, such as category, habitat, and focus spheres, and to manage the list of SOs relevant to their needs.
- Dynamic parameter selection and SO filtering
- Based on user inputs regarding site characteristics, the app filters the list of SOs to only include those relevant to the user’s specific conditions. Users can further refine this list by deselecting any SOs already covered or not needed.
- Cost calculation and data aggregation
- For the selected SOs, the app calculates various costs (e.g., purchase, maintenance, sampling, lab analysis) and aggregates this data to provide a comprehensive view of the financial requirements for implementing and maintaining the SOs at the user’s site.
- Visualization and insights
- Generates visualizations that offer insights into the cost distribution by type and sphere, as well as the total number of SOs required. These visualizations help users understand the financial and operational implications of their selections.
- Downloading results
- Provides options for users to download detailed cost breakdowns and visualizations. This feature allows for easy sharing and reporting of the findings generated by the app.
- User guidance
- Includes mechanisms for user guidance (e.g., tooltips) to ensure a smooth user experience and to provide assistance as needed.
Deployed version of the web application :globe_with_meridians:
You can access the current version of the Shiny app here.
Future hosting on eLTER service portal :motorway:
Upon completion and thorough testing, this tool will be hosted as part of the eLTER service portal. This integration aims to provide seamless access and utility for the eLTER community. Until then, this repository serves as the primary hub for development, where updates, enhancements, and bug fixes will be continuously pushed.
Reproducibility :repeat:
This repository utilizes the renv package to
manage R dependencies, ensuring that everyone working on the project has
access to the same package versions. By locking the project to specific
versions of R packages, renv ensures that the project can
be run consistently across different setups and over time.
Getting started :beginner:
When you clone or fork this repository for the first time, follow
these steps to set up renv:
- Install
renv(if you haven’t already)- You can install
renvglobally in your R setup using:
- You can install
install.packages("renv")- Clone the repository
- Clone this repository to your local machine.
- Launch R
- Open an R session and set the working directory to the root of the cloned repository.
- Restore the environment
- Install all the necessary packages, as specified in the
renv.lockfile, into a project-local library by running the following command in your R console:
- Install all the necessary packages, as specified in the
renv::restore()- Start working
- After the restoration process is complete, you can start working on
the project. The
renvenvironment will automatically be activated when you open the project in the future.
- After the restoration process is complete, you can start working on
the project. The
Citation :memo:
Souza, A. T., Ashraful Alam, S., Rasilo, T., Zacharias, S., & Bäck, J. (2024). eLTER SO Costs web application (Version 0.1.0) [Computer software]. https://doi.org/10.5281/zenodo.10948558
Acknowledgements :bank: :eu:
This work has been supported by the European Union’s H2020 (grant agreement No 871128 - eLTER PLUS).