eLTER SO Costs web application

Quick Links

• Authors
• CRediT author statement
• Access policy
• Context and aims
• Input data
• Structure of files
• Development
• Reproducibility
• Citation
• Acknowledgements
• Related resources

Authors 👥

• Name: Allan T. Souza

  • Affiliation: Institute for Atmospheric and Earth System Research (INAR), Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland 🇫🇮
  • Institution ROR: https://ror.org/040af2s02
  • E-mail: [email protected] / [email protected]
  • ORCID: 0000-0002-1851-681X

• Name: Syed Ashraful Alam

  • Affiliation: Institute for Atmospheric and Earth System Research (INAR), Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland 🇫🇮
  • Institution ROR: https://ror.org/040af2s02
  • E-mail: [email protected]
  • ORCID: 0000-0001-9870-1494

• Name: Terhi Rasilo

  • Affiliation: Institute for Atmospheric and Earth System Research (INAR), Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland 🇫🇮
  • Institution ROR: https://ror.org/040af2s02
  • E-mail: [email protected]
  • ORCID: 0000-0002-3502-4040

• Name: Steffen Zacharias

  • Affiliation: Department for Monitoring and Exploration Technologies, UFZ—Helmholtz Centre for Environmental Research GmbH, Leipzig, Germany 🇩🇪
  • Institution ROR: https://ror.org/000h6jb29
  • E-mail: [email protected]
  • ORCID: 0000-0002-7825-0072

• Name: Jaana Bäck

  • Affiliation: Institute for Atmospheric and Earth System Research (INAR), Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland 🇫🇮
  • Institution ROR: https://ror.org/040af2s02
  • E-mail: [email protected]
  • ORCID: 0000-0002-6107-667X

CRediT author statement 👨‍🔬 👩‍🔬

Contributor	Contributions
Allan T. Souza	Conceptualization, Data Curation, Formal analysis, Methodology, Software, Validation, Visualization, Writing - Original Draft.
Syed Ashraful Alam	Conceptualization, Validation, Visualization, Writing - Review & Editing.
Terhi Rasilo	Conceptualization, Project Administration, Validation, Writing - Review & Editing.
Steffen Zacharias	Conceptualization, Data Curation, Investigation, Supervision, Validation, Writing - Review & Editing.
Jaana Bäck	Conceptualization, Data Curation, Funding Acquisition, Investigation, Project Administration, Resources, Supervision, Validation, Writing - Review & Editing.

Access policy ⚖️

• 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 📖 🎯

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 💾

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 📂

├── .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
├── eLTER-SO-costs_input-data-standardization.R # file to process the changes in input data
├── .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 environment

Development 👨‍💻

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 ⚙️

• 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.

• 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 🌐

You can access the current version of the Shiny app here.

Future hosting on eLTER service portal 🛣️

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 🔁

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 🔰

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 renv globally in your R setup using:

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.lock file, into a project-local library by running the following command in your R console:

renv::restore()

• Start working
  • After the restoration process is complete, you can start working on the project. The renv environment will automatically be activated when you open the project in the future.

Citation 📝

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 🏦 🇪🇺

This work has been supported by the European Union's H2020 (grant agreement No 871128 - eLTER PLUS).

Related resources 🖇️

• Zacharias, S. et al. (2021). Discussion paper on eLTER Standard Observations (eLTER SOs). Deliverable D3.1 EU Horizon 2020 eLTER PLUS Project, Grant agreement No. 871128.